Merge remote-tracking branch 'upstream/master'

doc/source/api/app/index.rst

@@ -0,0 +1,139 @@
+pyFAI.app package
+=================
+
+pyFAI.app.average module
+------------------------
+
+.. automodule:: pyFAI.app.average
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.benchmark module
+--------------------------
+
+.. automodule:: pyFAI.app.benchmark
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.calib module
+----------------------
+
+.. automodule:: pyFAI.app.calib
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.calib2 module
+-----------------------
+
+.. automodule:: pyFAI.app.calib2
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.check_calib module
+----------------------------
+
+.. automodule:: pyFAI.app.check_calib
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.detector2nexus module
+-------------------------------
+
+.. automodule:: pyFAI.app.detector2nexus
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.diff_map module
+-------------------------
+
+.. automodule:: pyFAI.app.diff_map
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.diff_tomo module
+--------------------------
+
+.. automodule:: pyFAI.app.diff_tomo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.drawmask module
+-------------------------
+
+.. automodule:: pyFAI.app.drawmask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.eiger_mask module
+---------------------------
+
+.. automodule:: pyFAI.app.eiger_mask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.integrate module
+--------------------------
+
+.. automodule:: pyFAI.app.integrate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.mx_calibrate module
+-----------------------------
+
+.. automodule:: pyFAI.app.mx_calibrate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.recalib module
+------------------------
+
+.. automodule:: pyFAI.app.recalib
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.saxs module
+---------------------
+
+.. automodule:: pyFAI.app.saxs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.setup module
+----------------------
+
+.. automodule:: pyFAI.app.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.app.waxs module
+---------------------
+
+.. automodule:: pyFAI.app.waxs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.app
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/detectors/index.rst

@@ -0,0 +1,10 @@
+pyFAI.detectors package
+=======================
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.detectors
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/engines/index.rst

@@ -0,0 +1,35 @@
+pyFAI.engines package
+=====================
+
+pyFAI.engines.CSR_engine module
+-------------------------------
+
+.. automodule:: pyFAI.engines.CSR_engine
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.engines.histogram_engine module
+-------------------------------------
+
+.. automodule:: pyFAI.engines.histogram_engine
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.engines.preproc module
+----------------------------
+
+.. automodule:: pyFAI.engines.preproc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.engines
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/ext/index.rst

@@ -0,0 +1,221 @@
+pyFAI.ext package
+=================
+
+pyFAI.ext.bilinear module
+-------------------------
+
+.. automodule:: pyFAI.ext.bilinear
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.fastcrc module
+------------------------
+
+.. automodule:: pyFAI.ext.fastcrc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.histogram module
+--------------------------
+
+.. automodule:: pyFAI.ext.histogram
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.inpainting module
+---------------------------
+
+.. automodule:: pyFAI.ext.inpainting
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.invert_geometry module
+--------------------------------
+
+.. automodule:: pyFAI.ext.invert_geometry
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.morphology module
+---------------------------
+
+.. automodule:: pyFAI.ext.morphology
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.preproc module
+------------------------
+
+.. automodule:: pyFAI.ext.preproc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.reconstruct module
+----------------------------
+
+.. automodule:: pyFAI.ext.reconstruct
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.relabel module
+------------------------
+
+.. automodule:: pyFAI.ext.relabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.setup module
+----------------------
+
+.. automodule:: pyFAI.ext.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.sparse_builder module
+-------------------------------
+
+.. automodule:: pyFAI.ext.sparse_builder
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.sparse_utils module
+-----------------------------
+
+.. automodule:: pyFAI.ext.sparse_utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitBBox module
+--------------------------
+
+.. automodule:: pyFAI.ext.splitBBox
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitBBoxCSR module
+-----------------------------
+
+.. automodule:: pyFAI.ext.splitBBoxCSR
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitBBoxLUT module
+-----------------------------
+
+.. automodule:: pyFAI.ext.splitBBoxLUT
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitPixel module
+---------------------------
+
+.. automodule:: pyFAI.ext.splitPixel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitPixelFull module
+-------------------------------
+
+.. automodule:: pyFAI.ext.splitPixelFull
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitPixelFullCSR module
+----------------------------------
+
+.. automodule:: pyFAI.ext.splitPixelFullCSR
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.splitPixelFullLUT module
+----------------------------------
+
+.. automodule:: pyFAI.ext.splitPixelFullLUT
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext.watershed module
+--------------------------
+
+.. automodule:: pyFAI.ext.watershed
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.ext
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.ext private package
+=========================
+
+:mod:`ext._bispev` Module
+-------------------------
+
+.. automodule:: pyFAI.ext._bispev
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ext._blob` Module
+-----------------------
+
+.. automodule:: pyFAI.ext._blob
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ext._convolution` Module
+------------------------------
+
+.. automodule:: pyFAI.ext._convolution
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ext._distortion` Module
+-----------------------------
+
+.. automodule:: pyFAI.ext._distortion
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ext._geometry` Module
+---------------------------
+
+.. automodule:: pyFAI.ext._geometry
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+:mod:`ext._tree` Module
+-----------------------
+
+.. automodule:: pyFAI.ext._tree
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/dialog.rst

@@ -0,0 +1,59 @@
+pyFAI.gui.dialog package
+========================
+
+pyFAI.gui.dialog.Detector3dDialog module
+----------------------------------------
+
+.. automodule:: pyFAI.gui.dialog.Detector3dDialog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.dialog.DetectorSelectorDialog module
+----------------------------------------------
+
+.. automodule:: pyFAI.gui.dialog.DetectorSelectorDialog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.dialog.GeometryDialog module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.dialog.GeometryDialog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.dialog.IntegrationMethodDialog module
+-----------------------------------------------
+
+.. automodule:: pyFAI.gui.dialog.IntegrationMethodDialog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.dialog.MessageBox module
+----------------------------------
+
+.. automodule:: pyFAI.gui.dialog.MessageBox
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.dialog.OpenClDeviceDialog module
+------------------------------------------
+
+.. automodule:: pyFAI.gui.dialog.OpenClDeviceDialog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui.dialog
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/helper.rst

@@ -0,0 +1,75 @@
+pyFAI.gui.helper package
+========================
+
+pyFAI.gui.helper.MarkerManager module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.helper.MarkerManager
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.ProcessingWidget module
+----------------------------------------
+
+.. automodule:: pyFAI.gui.helper.ProcessingWidget
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.RingCalibration module
+---------------------------------------
+
+.. automodule:: pyFAI.gui.helper.RingCalibration
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.RingExtractor module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.helper.RingExtractor
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.SynchronizeMaskToolColor module
+------------------------------------------------
+
+.. automodule:: pyFAI.gui.helper.SynchronizeMaskToolColor
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.SynchronizePlotBackground module
+-------------------------------------------------
+
+.. automodule:: pyFAI.gui.helper.SynchronizePlotBackground
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.SynchronizeRawView module
+------------------------------------------
+
+.. automodule:: pyFAI.gui.helper.SynchronizeRawView
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.helper.model_transform module
+---------------------------------------
+
+.. automodule:: pyFAI.gui.helper.model_transform
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui.helper
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/index.rst

@@ -0,0 +1,103 @@
+pyFAI.gui package
+=================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    dialog
+    helper
+    model
+    tasks
+    utils
+    widgets
+
+pyFAI.gui.ApplicationContext module
+-----------------------------------
+
+.. automodule:: pyFAI.gui.ApplicationContext
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.CalibrationContext module
+-----------------------------------
+
+.. automodule:: pyFAI.gui.CalibrationContext
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.CalibrationWindow module
+----------------------------------
+
+.. automodule:: pyFAI.gui.CalibrationWindow
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.IntegrationDialog module
+----------------------------------
+
+.. automodule:: pyFAI.gui.IntegrationDialog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.cli_calibration module
+--------------------------------
+
+.. automodule:: pyFAI.gui.cli_calibration
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.diffmap_widget module
+-------------------------------
+
+.. automodule:: pyFAI.gui.diffmap_widget
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.jupyter module
+------------------------
+
+.. automodule:: pyFAI.gui.jupyter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.matplotlib module
+---------------------------
+
+.. automodule:: pyFAI.gui.matplotlib
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.peak_picker module
+----------------------------
+
+.. automodule:: pyFAI.gui.peak_picker
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.setup module
+----------------------
+
+.. automodule:: pyFAI.gui.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/model.rst

@@ -0,0 +1,179 @@
+pyFAI.gui.model package
+=======================
+
+pyFAI.gui.model.AbstractModel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.model.AbstractModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.CalibrantModel module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.model.CalibrantModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.CalibrationModel module
+---------------------------------------
+
+.. automodule:: pyFAI.gui.model.CalibrationModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.ConstraintModel module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.model.ConstraintModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.DataModel module
+--------------------------------
+
+.. automodule:: pyFAI.gui.model.DataModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.DataModelAdaptor module
+---------------------------------------
+
+.. automodule:: pyFAI.gui.model.DataModelAdaptor
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.DetectorModel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.model.DetectorModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.ExperimentSettingsModel module
+----------------------------------------------
+
+.. automodule:: pyFAI.gui.model.ExperimentSettingsModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.FilenameModel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.model.FilenameModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.Fit2dGeometryModel module
+-----------------------------------------
+
+.. automodule:: pyFAI.gui.model.Fit2dGeometryModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.GeometryConstraintsModel module
+-----------------------------------------------
+
+.. automodule:: pyFAI.gui.model.GeometryConstraintsModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.GeometryHistoryModel module
+-------------------------------------------
+
+.. automodule:: pyFAI.gui.model.GeometryHistoryModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.GeometryModel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.model.GeometryModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.ImageModel module
+---------------------------------
+
+.. automodule:: pyFAI.gui.model.ImageModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.IntegrationSettingsModel module
+-----------------------------------------------
+
+.. automodule:: pyFAI.gui.model.IntegrationSettingsModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.ListModel module
+--------------------------------
+
+.. automodule:: pyFAI.gui.model.ListModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.MarkerModel module
+----------------------------------
+
+.. automodule:: pyFAI.gui.model.MarkerModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.MaskedImageModel module
+---------------------------------------
+
+.. automodule:: pyFAI.gui.model.MaskedImageModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.PeakModel module
+--------------------------------
+
+.. automodule:: pyFAI.gui.model.PeakModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.PeakSelectionModel module
+-----------------------------------------
+
+.. automodule:: pyFAI.gui.model.PeakSelectionModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.model.PlotViewModel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.model.PlotViewModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui.model
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/tasks.rst

@@ -0,0 +1,59 @@
+pyFAI.gui.tasks package
+=======================
+
+pyFAI.gui.tasks.AbstractCalibrationTask module
+----------------------------------------------
+
+.. automodule:: pyFAI.gui.tasks.AbstractCalibrationTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.tasks.ExperimentTask module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.tasks.ExperimentTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.tasks.GeometryTask module
+-----------------------------------
+
+.. automodule:: pyFAI.gui.tasks.GeometryTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.tasks.IntegrationTask module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.tasks.IntegrationTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.tasks.MaskTask module
+-------------------------------
+
+.. automodule:: pyFAI.gui.tasks.MaskTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.tasks.PeakPickingTask module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.tasks.PeakPickingTask
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui.tasks
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/utils.rst

@@ -0,0 +1,107 @@
+pyFAI.gui.utils package
+=======================
+
+pyFAI.gui.utils.FilterBuilder module
+------------------------------------
+
+.. automodule:: pyFAI.gui.utils.FilterBuilder
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.ProxyAction module
+----------------------------------
+
+.. automodule:: pyFAI.gui.utils.ProxyAction
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.colorutils module
+---------------------------------
+
+.. automodule:: pyFAI.gui.utils.colorutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.eventutils module
+---------------------------------
+
+.. automodule:: pyFAI.gui.utils.eventutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.imageutils module
+---------------------------------
+
+.. automodule:: pyFAI.gui.utils.imageutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.projecturl module
+---------------------------------
+
+.. automodule:: pyFAI.gui.utils.projecturl
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.setup module
+----------------------------
+
+.. automodule:: pyFAI.gui.utils.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.timeutils module
+--------------------------------
+
+.. automodule:: pyFAI.gui.utils.timeutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.tree module
+---------------------------
+
+.. automodule:: pyFAI.gui.utils.tree
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.units module
+----------------------------
+
+.. automodule:: pyFAI.gui.utils.units
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.unitutils module
+--------------------------------
+
+.. automodule:: pyFAI.gui.utils.unitutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.utils.validators module
+---------------------------------
+
+.. automodule:: pyFAI.gui.utils.validators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/gui/widgets.rst

@@ -0,0 +1,195 @@
+pyFAI.gui.widgets package
+=========================
+
+pyFAI.gui.widgets.AdvancedComboBox module
+-----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.AdvancedComboBox
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.AdvancedSpinBox module
+----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.AdvancedSpinBox
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.CalibrantPreview module
+-----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.CalibrantPreview
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.CalibrantSelector module
+------------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.CalibrantSelector
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.ChoiceToolButton module
+-----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.ChoiceToolButton
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.ColoredCheckBox module
+----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.ColoredCheckBox
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.DetectorLabel module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.DetectorLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.DetectorModel module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.DetectorModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.DetectorSelector module
+-----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.DetectorSelector
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.ElidedLabel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.ElidedLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.FileEdit module
+---------------------------------
+
+.. automodule:: pyFAI.gui.widgets.FileEdit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.FitParamView module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.FitParamView
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.GeometryHistoryComboBox module
+------------------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.GeometryHistoryComboBox
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.GeometryLabel module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.GeometryLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.LoadImageToolButton module
+--------------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.LoadImageToolButton
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.MethodLabel module
+------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.MethodLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.MonitorNameEdit module
+----------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.MonitorNameEdit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.OpenClDeviceLabel module
+------------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.OpenClDeviceLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.QuantityEdit module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.QuantityEdit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.QuantityLabel module
+--------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.QuantityLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.UnitLabel module
+----------------------------------
+
+.. automodule:: pyFAI.gui.widgets.UnitLabel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.UnitSelector module
+-------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.UnitSelector
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.gui.widgets.WorkerConfigurator module
+-------------------------------------------
+
+.. automodule:: pyFAI.gui.widgets.WorkerConfigurator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.gui.widgets
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/io/index.rst

@@ -0,0 +1,35 @@
+pyFAI.io package
+================
+
+pyFAI.io.image module
+---------------------
+
+.. automodule:: pyFAI.io.image
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.io.integration_config module
+----------------------------------
+
+.. automodule:: pyFAI.io.integration_config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.io.ponifile module
+------------------------
+
+.. automodule:: pyFAI.io.ponifile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.io
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/modules.rst

@@ -13,6 +13,6 @@ both the geometry (it inherits from Geometry, another class)
 and exposes important methods (functions) like integrate1d and integrate2d.
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 2
 
    pyFAI

doc/source/api/opencl/index.rst

@@ -0,0 +1,75 @@
+pyFAI.opencl package
+====================
+
+pyFAI.opencl.OCLFullSplit module
+--------------------------------
+
+.. automodule:: pyFAI.opencl.OCLFullSplit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.azim_csr module
+----------------------------
+
+.. automodule:: pyFAI.opencl.azim_csr
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.azim_hist module
+-----------------------------
+
+.. automodule:: pyFAI.opencl.azim_hist
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.azim_lut module
+----------------------------
+
+.. automodule:: pyFAI.opencl.azim_lut
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.ocl_hist_pixelsplit module
+---------------------------------------
+
+.. automodule:: pyFAI.opencl.ocl_hist_pixelsplit
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.preproc module
+---------------------------
+
+.. automodule:: pyFAI.opencl.preproc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.setup module
+-------------------------
+
+.. automodule:: pyFAI.opencl.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.opencl.sort module
+------------------------
+
+.. automodule:: pyFAI.opencl.sort
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.opencl
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/pyFAI.rst

@@ -1,3 +1,17 @@
+pyFAI package
+=============
+
+.. toctree::
+
+    app/index
+    detectors/index
+    engines/index
+    ext/index
+    gui/index
+    io/index
+    opencl/index
+    resources/index
+    utils/index
 
 :mod:`pyFAI` Package
 --------------------
@@ -31,15 +45,6 @@
     :undoc-members:
     :show-inheritance:
 
-
-:mod:`integrate_widget` Module
-------------------------------
-
-.. automodule:: pyFAI.integrate_widget
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 :mod:`geometry` Module
 ----------------------
 
@@ -64,16 +69,6 @@
     :undoc-members:
     :show-inheritance:
 
-
-
-:mod:`detectors` Module
------------------------
-
-.. automodule:: pyFAI.detectors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 :mod:`spline` Module
 --------------------
 
@@ -82,22 +77,6 @@
     :undoc-members:
     :show-inheritance:
 
-:mod:`io` Module
-----------------
-
-.. automodule:: pyFAI.io
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`calibration` Module
--------------------------
-
-.. automodule:: pyFAI.calibration
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 :mod:`control_points` Module
 ----------------------------
 
@@ -106,15 +85,6 @@
     :undoc-members:
     :show-inheritance:
 
-
-:mod:`peak_picker` Module
--------------------------
-
-.. automodule:: pyFAI.peak_picker
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 :mod:`massif` Module
 --------------------
 
@@ -155,307 +125,3 @@
     :members:
     :undoc-members:
     :show-inheritance:
-
-:mod:`units` Module
--------------------
-
-.. automodule:: pyFAI.units
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`utils.__init__` Module
-----------------------------
-
-Sub module with miscelaneous tools
-
-.. automodule:: pyFAI.utils.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`utils.bayes` Module
-.........................
-
-Tool for bayesian filtering-out of positive peaks
-
-.. automodule:: pyFAI.utils.bayes
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`utils.shell` Module
-.........................
-
-Contains the progress-bar in the shell command line
-
-.. automodule:: pyFAI.utils.shell
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`utils.stringutil` Module
-..............................
-
-Enhanced string formatter
-
-.. automodule:: pyFAI.utils.stringutil
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`opencl.__init__` Module
------------------------------
-
-Contains all OpenCL implementation.
-
-.. automodule:: pyFAI.opencl
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`opencl.common` Module
-...........................
-
-.. automodule:: pyFAI.opencl.common
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`opencl.processing` Module
-...............................
-
-.. automodule:: pyFAI.opencl.processing
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`opencl.preproc` Module
-............................
-
-.. automodule:: pyFAI.opencl.preproc
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`opencl.azim_hist` Module
-..............................
-
-.. automodule:: pyFAI.opencl.azim_hist
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`opencl.azim_lut` Module
-.............................
-
-.. automodule:: pyFAI.opencl.azim_lut
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`opencl.azim_csr` Module
-.............................
-
-.. automodule:: pyFAI.opencl.azim_csr
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`gui.__init__` Module
---------------------------
-
-.. automodule:: pyFAI.gui.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`gui.matplotlib` Module
-............................
-
-Initialize properly Matplotlib
-
-.. automodule:: pyFAI.gui.matplotlib
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`gui.qt` Module
-....................
-
-
-.. automodule:: pyFAI.gui.qt
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`gui.utils` Module
-.......................
-
-.. automodule:: pyFAI.gui.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.__init__` Module
---------------------------
-Sub-module with all Cython binary extensions
-
-.. automodule:: pyFAI.ext.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`ext.bilinear` Module
-..........................
-
-This extension makes a discrete 2D-array appear like a continuous function thanks
-to bilinear interpolations.
-
-.. automodule:: pyFAI.ext.bilinear
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext._bispev` Module
-.........................
-
-This extension is a re-implementation of bi-cubic spline evaluation from scipy
-
-.. automodule:: pyFAI.ext._bispev
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext._blob` Module
-.......................
-
-Blob detection is used to find peaks in images by performing subsequent blurs
-
-.. automodule:: pyFAI.ext._blob
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext._convolution` Module
-..............................
-
-Convolutions in real space are used to blurs images, used in blob-detection algorithm
-
-.. automodule:: pyFAI.ext._convolution
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext._distortion` Module
-.............................
-
-Distortion correction are correction are applied by Look-up table (or CSR)
-
-.. automodule:: pyFAI.ext._distortion
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext._geometry` Module
-...........................
-
-This extension is a fast-implementation for calculating the geometry, i.e. where
-every pixel of an array stays in space (x,y,z) or its (r, \chi) coordinates.
-
-.. automodule:: pyFAI.ext._geometry
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.histogram` Module
-...........................
-
-Re-implementation of the numpy.histogram, optimized for azimuthal integration.
-Deprecated, will be replaced by silx.math.histogramnd
-
-.. automodule:: pyFAI.ext.histogram
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.invert_geometry` Module
-.................................
-
-Allow the inversion of pixel coordinate --> radius/azimuthal
-with linear interpolation within the last pixel
-
-.. automodule:: pyFAI.ext.invert_geometry
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-:mod:`ext.morphology` Module
-............................
-
-The morphology extension provides a couple of binary morphology operations on images.
-They are also implemented in scipy.ndimage in the general case, but not as fast.
-
-.. automodule:: pyFAI.ext.morphology
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.reconstruct` Module
-.............................
-
-Very simple inpainting module for reconstructing the missing part of an image (masked)
-to be able to use more common algorithms.
-
-.. automodule:: pyFAI.ext.reconstruct
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.relabel` Module
-.........................
-
-Relabel regions, used to flag from largest regions to the smallest
-
-.. automodule:: pyFAI.ext.relabel
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.preproc` Module
-.........................
-
-Contains a preprocessing function in charge of the dark-current subtraction,
-flat-field normalization, ... taking care of masked values and normalization.
-
-.. automodule:: pyFAI.ext.preproc
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext._tree` Module
-.......................
-
-The tree is used in file hierarchy tree for the diff_map graphical user interface.
-
-.. automodule:: pyFAI.ext._tree
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-:mod:`ext.watershed` Module
-...........................
-
-Peak peaking via inverse watershed for connecting region of high intensity
-
-.. automodule:: pyFAI.ext.watershed
-    :members:
-    :undoc-members:
-    :show-inheritance:

doc/source/api/resources/index.rst

@@ -0,0 +1,19 @@
+pyFAI.resources package
+=======================
+
+pyFAI.resources.setup module
+----------------------------
+
+.. automodule:: pyFAI.resources.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.resources
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/utils/index.rst

@@ -0,0 +1,91 @@
+pyFAI.utils package
+===================
+
+pyFAI.utils.bayes module
+------------------------
+
+.. automodule:: pyFAI.utils.bayes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.decorators module
+-----------------------------
+
+.. automodule:: pyFAI.utils.decorators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.ellipse module
+--------------------------
+
+.. automodule:: pyFAI.utils.ellipse
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.header_utils module
+-------------------------------
+
+.. automodule:: pyFAI.utils.header_utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.logging_utils module
+--------------------------------
+
+.. automodule:: pyFAI.utils.logging_utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.mathutil module
+---------------------------
+
+.. automodule:: pyFAI.utils.mathutil
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.orderedset module
+-----------------------------
+
+.. automodule:: pyFAI.utils.orderedset
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.setup module
+------------------------
+
+.. automodule:: pyFAI.utils.setup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.shell module
+------------------------
+
+.. automodule:: pyFAI.utils.shell
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyFAI.utils.stringutil module
+-----------------------------
+
+.. automodule:: pyFAI.utils.stringutil
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyFAI.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/geometry_conversion.rst

@@ -3,6 +3,8 @@
 :Keywords: geometry conversion from/to pyFAI
 :Target: developers
 
+.. _geometryconversion:
+
 The purpose of this note is to compare how ``pyFAI`` and ``ImageD11``
 treat the detector position. In particular, we derive how “PONI”
 detector parameters refined with ``pyFAI`` can be transformed into

doc/source/man/pyFAI-calib2.rst

@@ -13,16 +13,16 @@ without a priori knowledge of your setup. You will need to provide a calibrant
 or a "d-spacing" file containing the spacing of Miller plans in Angstrom
 (in decreasing order).
 
-Calibrants available: Ni, CrOx, NaCl,  Si_SRM640e,  Si_SRM640d,  Si_SRM640a,
-Si_SRM640c,  alpha_Al2O3,  Cr2O3,  AgBh,  Si_SRM640,  CuO,  PBBA,
-Si_SRM640b,  mock,  quartz, C14H30O, cristobaltite, Si, LaB6, CeO2, LaB6_SRM660a,
-LaB6_SRM660b, LaB6_SRM660c, TiO2, ZnO, Al, Au or search in the
-American Mineralogist database: http://rruff.geo.arizona.edu/AMS/amcsd.php
+Calibrants available: ``Ni``, ``CrOx``, ``NaCl``, ``Si_SRM640e``, ``Si_SRM640d``, ``Si_SRM640a``,
+``Si_SRM640c``, ``alpha_Al2O3``, ``Cr2O3``, ``AgBh``, ``Si_SRM640``, ``CuO``, ``PBBA``,
+``Si_SRM640b``, ``quartz``, ``C14H30O``, ``cristobaltite``, ``Si``, ``LaB6``, ``CeO2``, ``LaB6_SRM660a``,
+``LaB6_SRM660b``, ``LaB6_SRM660c``, ``TiO2``, ``ZnO``, ``Al``, ``Au`` or search in the
+`American Mineralogist database <http://rruff.geo.arizona.edu/AMS/amcsd.php>`_.
 
 Usage:
 ------
 
-pyFAI-calib2 [options] [input_image.edf]
+``pyFAI-calib2 [options] [input_image.edf]``
 
 Everything can be set by the GUI, but here are the command-line arguments.
 
@@ -30,171 +30,97 @@ Options:
 --------
 
    positional arguments:
-       FILE   List of files to calibrate
+     FILE                  List of files to calibrate
 
    optional arguments:
-       -h, --help
-              show this help message and exit
-
-       -V, --version
-              show program's version number and exit
-
-       -o FILE, --out FILE
-              Filename where processed image is saved
-
-       -v, --verbose
-              switch to debug/verbose mode
-
-       --debug
-              Set logging system in debug mode
-
-       -c FILE, --calibrant FILE
-              Calibrant name or file containing d-spacing of the reference sample (case sensitive)
-
-       -w WAVELENGTH, --wavelength WAVELENGTH
-              wavelength of the X-Ray beam in Angstrom.
-
-       -e ENERGY, --energy ENERGY
-              energy of the X-Ray beam in keV (hc=12.3984197396keV.A).
-
-       -P POLARIZATION_FACTOR, --polarization POLARIZATION_FACTOR
-              polarization factor, from -1 (vertical) to +1 (horizontal), default is None (no correction), synchrotrons are around 0.95
-
-       -D DETECTOR_NAME, --detector DETECTOR_NAME
-              Detector name (instead of pixel size+spline)
-
-       -m MASK, --mask MASK
-              file containing the mask (for image reconstruction)
-
-       -p PIXEL, --pixel PIXEL
-              size of the pixel in micron
-
-       -i FILE, --poni FILE
-              file containing the diffraction parameter (poni-file).
-
-       -b BACKGROUND, --background BACKGROUND
-              Automatic background subtraction if no value are provided
-
-       -d DARK, --dark DARK
-              list of comma separated dark images to average and subtract
-
-       -f FLAT, --flat FLAT
-              list of comma separated flat images to average and divide
-
-       -s SPLINE, --spline SPLINE
-              spline file describing the detector distortion
-
-       -n NPT, --pt NPT
-              file with datapoints saved. Default: basename.npt
-
-       --filter FILTER
-              select the filter, either mean(default), max or median
-
-       -l DISTANCE, --distance DISTANCE
-              sample-detector distance in millimeter. Default: 100mm
-
-       --dist DIST
-              sample-detector distance in meter. Default: 0.1m
-
-       --poni1 PONI1
-              poni1 coordinate in meter. Default: center of detector
-
-       --poni2 PONI2
-              poni2 coordinate in meter. Default: center of detector
-
-       --rot1 ROT1
-              rot1 in radians. default: 0
-
-       --rot2 ROT2
-              rot2 in radians. default: 0
-
-       --rot3 ROT3
-              rot3 in radians. default: 0
-
-       --fix-wavelength
-              fix the wavelength parameter. Default: Activated
-
-       --free-wavelength
-              free the wavelength parameter. Default: Deactivated
-
-       --fix-dist
-              fix the distance parameter
-
-       --free-dist
-              free the distance parameter. Default: Activated
-
-       --fix-poni1
-              fix the poni1 parameter
-
-       --free-poni1
-              free the poni1 parameter. Default: Activated
-
-       --fix-poni2
-              fix the poni2 parameter
-
-       --free-poni2
-              free the poni2 parameter. Default: Activated
-
-       --fix-rot1
-              fix the rot1 parameter
-
-       --free-rot1
-              free the rot1 parameter. Default: Activated
-
-       --fix-rot2
-              fix the rot2 parameter
-
-       --free-rot2
-              free the rot2 parameter. Default: Activated
-
-       --fix-rot3
-              fix the rot3 parameter
-
-       --free-rot3
-              free the rot3 parameter. Default: Activated
-
-       --npt NPT_1D
-              Number of point in 1D integrated pattern, Default: 1024
-
-       --npt-azim NPT_2D_AZIM
-              Number of azimuthal sectors in 2D integrated images.  Default: 360
-
-       --npt-rad NPT_2D_RAD
-              Number of radial bins in 2D integrated images.  Default: 400
-
-       --qtargs QTARGS
-              Arguments propagated to Qt
-
-       --tilt Allow initially detector tilt to be refined (rot1, rot2, rot3). Default: Activated
-
-       --no-tilt
-              Deactivated tilt refinement and set all rotation to 0
-
-       --saturation SATURATION
-              consider all pixel>max*(1-saturation) as saturated and reconstruct them, default: 0 (deactivated)
-
-       --weighted
-              weight fit by intensity, by default not.
-
-       --unit UNIT
-              Valid units for radial range: 2th_deg, 2th_rad, q_nm^-1, q_A^-1, r_mm. Default: 2th_deg
-
-       --no-gui
-              force the program to run without a Graphical interface
-
-       --no-interactive
-              force the program to run and exit without prompting for refinements
-
-       -r, --reconstruct
-              Reconstruct image where data are masked or <0 (for Pilatus detectors or detectors with modules)
-
-       -g GAUSSIAN, --gaussian GAUSSIAN
-              Size of the gaussian kernel. Size of the gap (in pixels) between two consecutive rings, by default 100 Increase the value if the arc is not complete; decrease the  value  if  arcs  are  mixed
-              together.
-
-       --square
-              Use square kernel shape for neighbor search instead of diamond shape
-
+     -h, --help            show this help message and exit
+     -V, --version         show program's version number and exit
+     -o FILE, --out FILE   Filename where processed image is saved
+     -v, --verbose         switch to debug/verbose mode
+     --debug               Set logging system in debug mode
+     --opengl, --gl        Enable OpenGL rendering (else matplotlib is used)
+     -c FILE, --calibrant FILE
+                           Calibrant name or file containing d-spacing of the
+                           reference sample (case sensitive)
+     -w WAVELENGTH, --wavelength WAVELENGTH
+                           wavelength of the X-Ray beam in Angstrom.
+     -e ENERGY, --energy ENERGY
+                           energy of the X-Ray beam in keV
+                           (hc=12.398419739640717keV.A).
+     -P POLARIZATION_FACTOR, --polarization POLARIZATION_FACTOR
+                           polarization factor, from -1 (vertical) to +1
+                           (horizontal), default is None (no correction),
+                           synchrotrons are around 0.95
+     -D DETECTOR_NAME, --detector DETECTOR_NAME
+                           Detector name (instead of pixel size+spline)
+     -m MASK, --mask MASK  file containing the mask (for image reconstruction)
+     -p PIXEL, --pixel PIXEL
+                           size of the pixel in micron
+     -s SPLINE, --spline SPLINE
+                           spline file describing the detector distortion
+     -n NPT, --pt NPT      file with datapoints saved. Example: basename.npt
+     -i FILE, --poni FILE  file containing the diffraction parameter (poni-file)
+                           [not used].
+     -b BACKGROUND, --background BACKGROUND
+                           Automatic background subtraction if no value are
+                           provided [not used]
+     -d DARK, --dark DARK  list of comma separated dark images to average and
+                           subtract [not used]
+     -f FLAT, --flat FLAT  list of comma separated flat images to average and
+                           divide [not used]
+     --filter FILTER       select the filter, either mean(default), max or median
+                           [not used]
+     -l DIST_MM, --distance DIST_MM
+                           sample-detector distance in millimeter. Default: 100mm
+     --dist DIST           sample-detector distance in meter. Default: 0.1m
+     --poni1 PONI1         poni1 coordinate in meter. Default: center of detector
+     --poni2 PONI2         poni2 coordinate in meter. Default: center of detector
+     --rot1 ROT1           rot1 in radians. default: 0
+     --rot2 ROT2           rot2 in radians. default: 0
+     --rot3 ROT3           rot3 in radians. default: 0
+     --fix-wavelength      fix the wavelength parameter. Default: Activated
+     --free-wavelength     free the wavelength parameter. Default: Deactivated
+     --fix-dist            fix the distance parameter
+     --free-dist           free the distance parameter. Default: Activated
+     --fix-poni1           fix the poni1 parameter
+     --free-poni1          free the poni1 parameter. Default: Activated
+     --fix-poni2           fix the poni2 parameter
+     --free-poni2          free the poni2 parameter. Default: Activated
+     --fix-rot1            fix the rot1 parameter
+     --free-rot1           free the rot1 parameter. Default: Activated
+     --fix-rot2            fix the rot2 parameter
+     --free-rot2           free the rot2 parameter. Default: Activated
+     --fix-rot3            fix the rot3 parameter
+     --free-rot3           free the rot3 parameter. Default: Activated
+     --npt NPT_1D          Number of point in 1D integrated pattern, Default:
+                           1024
+     --npt-azim NPT_2D_AZIM
+                           Number of azimuthal sectors in 2D integrated images.
+                           Default: 360
+     --npt-rad NPT_2D_RAD  Number of radial bins in 2D integrated images.
+                           Default: 400
+     --qtargs QTARGS       Arguments propagated to Qt
+     --tilt                Allow initially detector tilt to be refined (rot1,
+                           rot2, rot3). Default: Activated
+     --no-tilt             Deactivated tilt refinement and set all rotation to 0
+     --saturation SATURATION
+                           consider all pixel>max*(1-saturation) as saturated and
+                           reconstruct them, default: 0 (deactivated)
+     --weighted            weight fit by intensity, by default not.
+     --unit UNIT           Valid units for radial range: 2th_deg, 2th_rad,
+                           q_nm^-1, q_A^-1, r_mm. Default: 2th_deg
+     --no-gui              force the program to run without a Graphical interface
+     --no-interactive      force the program to run and exit without prompting
+                           for refinements
+     -r, --reconstruct     Reconstruct image where data are masked or <0 (for
+                           Pilatus detectors or detectors with modules)
+     -g GAUSSIAN, --gaussian GAUSSIAN
+                           Size of the gaussian kernel. Size of the gap (in
+                           pixels) between two consecutive rings, by default 100
+                           Increase the value if the arc is not complete;
+                           decrease the value if arcs are mixed together.
+     --square              Use square kernel shape for neighbor search instead of
+                           diamond shape
 
 Tips & Tricks
 -------------

doc/source/man/pyFAI-drawmask.rst

@@ -1,6 +1,8 @@
 Mask generation tool: pyFAI-drawmask
 ====================================
 
+.. _pyFAI-drawmask:
+
 Purpose
 -------
 

doc/source/man/pyFAI-integrate.rst

@@ -4,7 +4,7 @@ Integration tool: pyFAI-integrate
 Purpose
 -------
 
-PyFAI-integrate is a graphical interface (based on Python/Qt4) to perform azimuthal integration
+PyFAI-integrate is a graphical interface (based on Python/Qt5) to perform azimuthal integration
 on a set of files. It exposes most of the important options available within pyFAI and allows you
 to select a GPU (or an openCL platform) to perform the calculation on.
 
@@ -16,36 +16,46 @@ to select a GPU (or an openCL platform) to perform the calculation on.
 Usage
 -----
 
-pyFAI-integrate [options] file1.edf file2.edf ...
+``pyFAI-integrate [options] file1.edf file2.edf ...``
 
 Options:
 --------
 
-  -h, --help            show this help message and exit
-  -V, --version         show program's version number and exit
-  -v, --verbose         switch to verbose/debug mode
-  -o OUTPUT, --output OUTPUT
-                        Directory or file where to store the output data
-  -f FORMAT, --format FORMAT
-                        output data format (can be HDF5)
-  -s SLOW, --slow-motor SLOW
-                        Dimension of the scan on the slow direction (makes
-                        sense only with HDF5)
-  -r RAPID, --fast-motor RAPID
-                        Dimension of the scan on the fast direction (makes
-                        sense only with HDF5)
-  --no-gui              Process the dataset without showing the user
-                        interface.
-  -j JSON, --json JSON  Configuration file containing the processing to be
-                        done
-  --monitor-name MONITOR_KEY
-                        Name of the monitor in the header of each input files.
-                        If defined the contribution of each input file is
-                        divided by the monitor. If the header does not contain
-                        or contains a wrong value, the contribution of the
-                        input file is ignored. On EDF files, values from
-                        'counter_pos' can accessed by using the expected
-                        mnemonic. For example 'counter/bmon'.
+	positional arguments:
+	  FILE                  Files to be integrated
+
+	optional arguments:
+	  -h, --help            show this help message and exit
+	  -V, --version         show program's version number and exit
+	  -v, --verbose         switch to verbose/debug mode
+	  --debug               Set logging system in debug mode
+	  -o OUTPUT, --output OUTPUT
+	                        Directory or file where to store the output data
+	  -f FORMAT, --format FORMAT
+	                        output data format (can be HDF5)
+	  -s SLOW, --slow-motor SLOW
+	                        Dimension of the scan on the slow direction (makes
+	                        sense only with HDF5)
+	  -r RAPID, --fast-motor RAPID
+	                        Dimension of the scan on the fast direction (makes
+	                        sense only with HDF5)
+	  --no-gui              Process the dataset without showing the user
+	                        interface.
+	  -j JSON, --json JSON  Configuration file containing the processing to be
+	                        done
+	  --monitor-name MONITOR_KEY
+	                        Name of the monitor in the header of each input files.
+	                        If defined the contribution of each input file is
+	                        divided by the monitor. If the header does not contain
+	                        or contains a wrong value, the contribution of the
+	                        input file is ignored. On EDF files, values from
+	                        'counter_pos' can be accessed by using the expected
+	                        mnemonic. For example 'counter/bmon'.
+	  --delete              Delete the destination file if already exists
+	  --append              Append the processing to the destination file using an
+	                        available group (HDF5 output)
+	  --overwrite           Overwrite the entry of the destination file if it
+	                        already exists (HDF5 output)
 
 Tips & Tricks:
 --------------
@@ -53,6 +63,3 @@ Tips & Tricks:
 PyFAI-integrate saves all parameters in a .azimint.json (hidden) file. This JSON file
 is an ascii file which can be edited and used to configure online data analysis using
 the LImA plugin of pyFAI.
-
-Nota: there is bug in debian6 making the GUI crash (to be fixed inside pyqt)
-http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=697348

doc/source/man/scripts.rst

@@ -15,21 +15,21 @@ The calibration is the determination of the geometry of the experimental setup u
 Finally a full dataset can be integrated using different tools targeted at different experiments.
 
 Pre-processing tools:
- * pyFAI-drawmask: tool for drawing a mask on top of an image
- * pyFAI-average: tool for averaging/median/... filtering images (i.e. for dark current)
+ * ``pyFAI-drawmask``: tool for drawing a mask on top of an image (deprecated)
+ * ``pyFAI-average``: tool for averaging/median/... filtering images (i.e. for dark current)
 
 Calibration tools:
- * pyFAI-calib: manually select the rings and refine the geometry
- * pyFAI-recalib: automatic ring extraction to refine the geometry (deprecated: see "recalib" option in pyFAI-calib)
- * MX-calibrate: Calibrate automatically a set of images taken at various detector distances
- * check_calib: checks the calibration of an image at the sub-pixel level (deprecated: see "validate" option in pyFAI-calib)
+ * ``pyFAI-calib2`` and ``pyFAI-calib``: manually select the rings and refine the geometry
+ * ``pyFAI-recalib``: automatic ring extraction to refine the geometry (deprecated: see "recalib" option in pyFAI-calib)
+ * ``MX-calibrate``: Calibrate automatically a set of images taken at various detector distances
+ * ``check_calib``: checks the calibration of an image at the sub-pixel level (deprecated: see "validate" option in pyFAI-calib)
 
 Azimuthal integration tools:
- * pyFAI-integrate: the graphical interface for integration (GUI)
- * pyFAI-saxs: command line interface for small-angle scattering
- * pyFAI-waxs: command line interface for powder difration
- * diff_map: diffraction mapping & tomography tool (command line and GUI)
- * diff_tomo: diffraction tomography tool (command line only)
+ * ``pyFAI-integrate``: the graphical interface for integration (GUI)
+ * ``pyFAI-saxs``: command line interface for small-angle scattering
+ * ``pyFAI-waxs``: command line interface for powder difration
+ * ``diff_map``: diffraction mapping & tomography tool (command line and GUI)
+ * ``diff_tomo``: diffraction tomography tool (command line only)
 
 .. toctree::
    :maxdepth: 1

doc/source/pyFAI.rst

@@ -61,10 +61,10 @@ implemente from scratch a novel azimuthal integration tool which is
 designed to take advantage of modern parallel hardware features.
 PyFAI assumes the setup does not change during the experiment and tries to reuse
 a maximum number of data (using memoization_), moreover those calculation are performed
-only when needed (lazy_evaluation_).
+only when needed (`lazy evaluation`_).
 
 .. _memoization: http://en.wikipedia.org/wiki/Memoization
-.. _lazy_evaluation: http://en.wikipedia.org/wiki/Lazy_evaluation
+.. _lazy evaluation: http://en.wikipedia.org/wiki/Lazy_evaluation
 
 Experiment description
 ----------------------

pyFAI/app/average.py

@@ -33,7 +33,7 @@ __author__ = "Jerome Kieffer, Picca Frédéric-Emmanuel"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "01/03/2019"
+__date__ = "17/05/2019"
 __status__ = "production"
 
 import os
@@ -99,8 +99,8 @@ def parse_algorithms(options):
 def cleanup_input_paths(input_paths):
     """Clean up filename using :: to access to data inside file.
 
-    :returns: Returns a list of paths without directory separator inside the filename
-    location.
+    :returns: Returns a list of paths without directory separator inside the
+        filename location.
     """
     result = []
     for path in input_paths:

pyFAI/app/drawmask.py

@@ -34,7 +34,7 @@ __authors__ = ["Jerome Kieffer", "Valentin Valls"]
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "09/05/2019"
+__date__ = "16/05/2019"
 __satus__ = "Production"
 
 import os
@@ -46,7 +46,6 @@ import fabio
 
 _logger = logging.getLogger("drawmask")
 
-import silx
 import silx.gui.plot
 from silx.gui import qt
 import pyFAI.utils
@@ -97,12 +96,7 @@ class MaskImageWidget(AbstractMaskImageWidget):
 
         self.__plot2D = silx.gui.plot.Plot2D()
         self.__plot2D.setKeepDataAspectRatio(True)
-        if hasattr(self.__plot2D, "getMaskAction"):
-            # silx 0.5 and later
-            maskAction = self.__plot2D.getMaskAction()
-        else:
-            # silx 0.4 and previous
-            maskAction = self.__plot2D.maskAction
+        maskAction = self.__plot2D.getMaskAction()
         maskAction.setVisible(False)
         self.__maskPanel = silx.gui.plot.MaskToolsWidget.MaskToolsWidget(plot=self.__plot2D)
         try:

pyFAI/engines/preproc.py

@@ -25,9 +25,7 @@
 #  THE SOFTWARE.
 
 
-"""Pre-Processing
-
-A module for all common pixel-wise  pre-processing of data.
+"""Module providing common pixel-wise pre-processing of data.
 """
 
 from __future__ import absolute_import, print_function, with_statement
@@ -36,7 +34,7 @@ __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "06/05/2019"
+__date__ = "17/05/2019"
 __status__ = "development"
 
 import warnings
@@ -87,10 +85,8 @@ def preproc(raw,
     NaN are always considered as invalid values
 
     if neither empty nor dummy is provided, empty pixels are 0.
-    Empty pixels are always zero in "split_result" mode
+    Empty pixels are always zero in "split_result" mode.
 
-    Split result:
-    -------------
     When set to False, i.e the default, the pixel-wise operation is:
     I = (raw - dark)/(flat \* solidangle \* polarization \* absorption)
     Invalid pixels are set to the dummy or empty value.
@@ -100,7 +96,7 @@ def preproc(raw,
     I = [(raw - dark), (variance), (flat \* solidangle \* polarization \* absorption)]
     Empty pixels will have all their 2 or 3 values to 0 (and not to dummy or empty value)
 
-    If poissonian is set to True, the variance is evaluated as (raw + dark)
+    If poissonian is set to True, the variance is evaluated as (raw + dark).
     """
     if isinstance(dtype, str):
         dtype = numpy.dtype(dtype).type

pyFAI/ext/__init__.py

@@ -0,0 +1,29 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (C) 2016-2018 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+"""Package containing all Cython binary extensions"""
+
+__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
+__license__ = "MIT"

pyFAI/ext/_bispev.pyx

@@ -25,14 +25,14 @@
 #  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
-'''Spline evaluation function
 
-Created on Nov 4, 2013
-'''
+
+"""Module containing a re-implementation of bi-cubic spline evaluation from
+scipy."""
 
 __authors__ = ["Zubair Nawaz", "Jerome Kieffer"]
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "15/11/2018"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 
@@ -51,13 +51,15 @@ def bisplev(x, y, tck, dx=0, dy=0):
     Return a rank-2 array of spline function values (or spline derivative
     values) at points given by the cross-product of the rank-1 arrays x and
     y.  In special cases, return an array or just a float if either x or y or
-    both are floats.  Based on BISPEV from FITPACK.
+    both are floats. Based on BISPEV from FITPACK.
 
     See :func:`bisplrep` to generate the `tck` representation.
 
     See also :func:`splprep`, :func:`splrep`, :func:`splint`, :func:`sproot`,
     :func:`splev`, :func:`UnivariateSpline`, :func:`BivariateSpline`
 
+    References: [1]_, [2]_, [3]_.
+
     .. [1] Dierckx P. : An algorithm for surface fitting
        with spline functions
        Ima J. Numer. Anal. 1 (1981) 267-283.

pyFAI/ext/_blob.pyx

@@ -25,12 +25,16 @@
 #  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
+
 """
-Some Cythonized function for blob detection function
+Some Cythonized function for blob detection function.
+
+It is used to find peaks in images by performing subsequent blurs.
 """
+
 __authors__ = ["Aurore Deschildre", "Jerome Kieffer"]
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "10/01/2018"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 import cython

pyFAI/ext/_convolution.pyx

@@ -26,11 +26,15 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
-"""Implementation of a separable 2D convolution"""
+"""Implementation of a separable 2D convolution.
+
+It is used in real space are used to blurs images, used in blob-detection
+algorithm.
+"""
 
 __authors__ = ["Pierre Paleo", "Jerome Kieffer"]
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "01/12/2016"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 import cython

pyFAI/ext/_distortion.pyx

@@ -26,9 +26,13 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
+"""
+Distortion correction are correction are applied by look-up table (or CSR)
+"""
+
 __author__ = "Jerome Kieffer"
 __license__ = "MIT"
-__date__ = "21/01/2019"
+__date__ = "17/05/2019"
 __copyright__ = "2011-2018, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"
 

pyFAI/ext/_geometry.pyx

@@ -26,9 +26,15 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
+"""
+This extension is a fast-implementation for calculating the geometry, i.e. where
+every pixel of an array stays in space (x,y,z) or its (r, :math:`\\chi`)
+coordinates.
+"""
+
 __author__ = "Jerome Kieffer"
 __license__ = "MIT"
-__date__ = "26/10/2018"
+__date__ = "17/05/2019"
 __copyright__ = "2011-2016, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"
 

pyFAI/ext/_tree.pyx

@@ -26,9 +26,12 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
+"""Module used in file hierarchy tree for the diff_map graphical user interface.
+"""
+
 __author__ = "Jerome Kieffer"
 __license__ = "MIT"
-__date__ = "09/01/2018"
+__date__ = "17/05/2019"
 __copyright__ = "2011-2015, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"
 

pyFAI/ext/bilinear.pyx

@@ -25,10 +25,13 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
+"""Module with makes a discrete 2D-array appear like a continuous function thanks
+to bilinear interpolations.
+"""
 
 __author__ = "Jerome Kieffer"
 __license__ = "MIT"
-__date__ = "18/04/2019"
+__date__ = "17/05/2019"
 __copyright__ = "2011-2015, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"
 

pyFAI/ext/histogram.pyx

@@ -26,10 +26,15 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
-"""A set of histogram functions with or without OpenMP enabled."""
+"""A set of histogram functions with or without OpenMP enabled.
+
+Re-implementation of the numpy.histogram, optimized for azimuthal integration.
+
+Deprecated, will be replaced by ``silx.math.histogramnd``.
+"""
 
 __author__ = "Jerome Kieffer"
-__date__ = "06/05/2019"
+__date__ = "17/05/2019"
 __license__ = "MIT"
 __copyright__ = "2011-2019, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"

pyFAI/ext/invert_geometry.pyx

@@ -25,9 +25,15 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
+
+"""
+Module providing inversion transformation from pixel coordinate to radial/azimuthal
+coordinate.
+"""
+
 __author__ = "Jerome Kieffer"
 __license__ = "MIT"
-__date__ = "06/05/2019"
+__date__ = "17/05/2019"
 __copyright__ = "2018-2018, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"
 

pyFAI/ext/morphology.pyx

@@ -26,12 +26,15 @@
 #  THE SOFTWARE.
 
 """
-A few binary morphology operation
+This module provides a couple of binary morphology operations on images.
+
+They are also implemented in ``scipy.ndimage`` in the general case, but not as
+fast.
 """
 
 __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "09/01/2018"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 

pyFAI/ext/new_diagram.uxf

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><umlet_diagram></umlet_diagram>

pyFAI/ext/preproc.pyx

@@ -25,10 +25,14 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
+"""
+Contains a preprocessing function in charge of the dark-current subtraction,
+flat-field normalization... taking care of masked values and normalization.
+"""
 
 __author__ = "Jerome Kieffer"
 __license__ = "MIT"
-__date__ = "06/05/2019"
+__date__ = "17/05/2019"
 __copyright__ = "2011-2018, ESRF"
 __contact__ = "jerome.kieffer@esrf.fr"
 

pyFAI/ext/reconstruct.pyx

@@ -25,11 +25,15 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
-"""Cython module to reconstruct the masked values of an image"""
+"""Cython module to reconstruct the masked values of an image.
+
+It's a simple inpainting module for reconstructing the missing part of an
+image (masked) to be able to use more common algorithms.
+"""
 
 __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "15/11/2018"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 

pyFAI/ext/relabel.pyx

@@ -26,11 +26,14 @@
 #  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 #  THE SOFTWARE.
 
-"""A module to relabel regions"""
+"""Module providing features to relabel regions.
+
+It is used to flag from largest regions to the smallest.
+"""
 
 __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "15/11/2018"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 

pyFAI/ext/watershed.pyx

@@ -26,11 +26,12 @@
 #  THE SOFTWARE.
 
 #
-"""Inverse watershed for connecting region of high intensity
+"""Peak peaking via inverse watershed for connecting region of high intensity
 """
+
 __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.kieffer@esrf.fr"
-__date__ = "11/01/2018"
+__date__ = "17/05/2019"
 __status__ = "stable"
 __license__ = "MIT"
 

pyFAI/geometry.py

@@ -202,7 +202,7 @@ class Geometry(object):
         return os.linesep.join(lstTxt)
 
     def check_chi_disc(self, range):
-        """Check the position of the \chi discontinuity
+        """Check the position of the :math:`\\chi` discontinuity
 
         :param range: range of chi for the integration
         :return: True if there is a problem
@@ -998,7 +998,7 @@ class Geometry(object):
         """
         Calculate the incidence angle (alpha) for current pixels (P).
         The poni being the point of normal incidence,
-        it's incidence angle is $\{alpha} = 0$ hence $cos(\{alpha}) = 1$
+        it's incidence angle is :math:`\\{alpha} = 0` hence :math:`cos(\\{alpha}) = 1`.
 
         :param d1: 1d or 2d set of points in pixel coord
         :param d2:  1d or 2d set of points in pixel coord
@@ -1051,7 +1051,7 @@ class Geometry(object):
         .. math::
 
             dOmega = \\frac{Omega(P)}{Omega(C)}
-                   = \\frac{A \cdot cos(a)}{SP^2} \cdot \\frac{SC^2}{A \cdot cos(0)}
+                   = \\frac{A \\cdot cos(a)}{SP^2} \\cdot \\frac{SC^2}{A \\cdot cos(0)}
                    = \\frac{3}{cos(a)}
                    = \\frac{SC^3}{SP^3}
 

pyFAI/gui/cli_calibration.py

@@ -37,7 +37,7 @@ __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "17/12/2018"
+__date__ = "17/05/2019"
 __status__ = "production"
 
 import os
@@ -124,29 +124,29 @@ class AbstractCalibration(object):
                 " display too many images without crashing, this"\
                 " is why the window showing the diffraction image"\
                 " is closed"
-    HELP = {"help": "Try to get the help of a given action, like 'refine?'. Use done when finished. "
-            "Most command are composed of 'action parameter value' like 'set wavelength 1 A'.",
-            "get": "print he value of a parameter",
-            "set": "set the value of a parameter to the given value, i.e 'set wavelength 0.1 nm', units are optional",
-            'fix': "fixes the value of a parameter so that its value will not be optimized, i.e. 'fix wavelength'",
-            'free': "frees the parameter so that the value can be optimized, i.e. 'free wavelength'",
-            'bound': "sets the upper and lower bound of a parameter: 'bound dist 0.1 0.2'",
-            'bounds': "sets the upper and lower bound of all parameters",
-            'refine': "performs a new cycle of refinement",
-            'recalib': "extract a new set of rings and re-perform the calibration. One can specify how many rings to extract and the algorithm to use (blob, massif, watershed) and the nb_pts_per_deg in azimuth",
-            'done': "finishes the processing, performs an integration and quits",
-            'validate': "plot the offset between the calibrated image and the back-projected image",
-            'validate2': "measures the offset of the center as function of azimuthal angle by cross-correlation of 2 plots, 180 deg appart. Option: number of azimuthal sliced, default: 36",
-            'integrate': "perform the azimuthal integration and display results",
-            'abort': "quit immediately, discarding any unsaved changes",
-            'show': "Just print out the current parameter set. Optional parameters are units for length, rotation and wavelength, i.e. 'show mm deg A'",
-            'reset': "Reset the geometry to the initial guess (rotation to zero, distance to 0.1m, poni at the center of the image)",
-            'assign': "Change the assignment of a group of points to a rings",
-            "weight": "toggle from weighted to unweighted mode...",
-            "define": "Re-define the value for a constant internal parameter of the program like max_iter, nPt_1D, nPt_2D_azim, nPt_2D_rad, integrator_method, error_model. Warning: attribute change may be harmful !",
-            "chiplot": "plot control point radial error as function of azimuthal angle, optional parameters: the rings for which this need to be plotted",
-            "delete": "delete a group of points, provide the letter."
-            }
+    _HELP = {"help": "Try to get the help of a given action, like 'refine?'. Use done when finished. "
+             "Most command are composed of 'action parameter value' like 'set wavelength 1 A'.",
+             "get": "print he value of a parameter",
+             "set": "set the value of a parameter to the given value, i.e 'set wavelength 0.1 nm', units are optional",
+             'fix': "fixes the value of a parameter so that its value will not be optimized, i.e. 'fix wavelength'",
+             'free': "frees the parameter so that the value can be optimized, i.e. 'free wavelength'",
+             'bound': "sets the upper and lower bound of a parameter: 'bound dist 0.1 0.2'",
+             'bounds': "sets the upper and lower bound of all parameters",
+             'refine': "performs a new cycle of refinement",
+             'recalib': "extract a new set of rings and re-perform the calibration. One can specify how many rings to extract and the algorithm to use (blob, massif, watershed) and the nb_pts_per_deg in azimuth",
+             'done': "finishes the processing, performs an integration and quits",
+             'validate': "plot the offset between the calibrated image and the back-projected image",
+             'validate2': "measures the offset of the center as function of azimuthal angle by cross-correlation of 2 plots, 180 deg appart. Option: number of azimuthal sliced, default: 36",
+             'integrate': "perform the azimuthal integration and display results",
+             'abort': "quit immediately, discarding any unsaved changes",
+             'show': "Just print out the current parameter set. Optional parameters are units for length, rotation and wavelength, i.e. 'show mm deg A'",
+             'reset': "Reset the geometry to the initial guess (rotation to zero, distance to 0.1m, poni at the center of the image)",
+             'assign': "Change the assignment of a group of points to a rings",
+             "weight": "toggle from weighted to unweighted mode...",
+             "define": "Re-define the value for a constant internal parameter of the program like max_iter, nPt_1D, nPt_2D_azim, nPt_2D_rad, integrator_method, error_model. Warning: attribute change may be harmful !",
+             "chiplot": "plot control point radial error as function of azimuthal angle, optional parameters: the rings for which this need to be plotted",
+             "delete": "delete a group of points, provide the letter."
+             }
     PARAMETERS = ["dist", "poni1", "poni2", "rot1", "rot2", "rot3", "wavelength"]
     UNITS = {"dist": "meter", "poni1": "meter", "poni2": "meter", "rot1": "radian",
              "rot2": "radian", "rot3": "radian", "wavelength": "meter"}
@@ -795,15 +795,15 @@ class AbstractCalibration(object):
             if action in ["help", "?"]:
                 req_help = True
             if req_help:
-                for what in self.HELP.keys():
+                for what in self._HELP.keys():
                     if action.startswith(what):
                         print("Help on %s" % what)
-                        print(self.HELP[what])
+                        print(self._HELP[what])
                         break
                 else:
                     print("Help on commands")
-                    print(self.HELP["help"])
-                    print("Valid actions: " + ", ".join(self.HELP.keys()))
+                    print(self._HELP["help"])
+                    print("Valid actions: " + ", ".join(self._HELP.keys()))
                     print("Valid parameters: " + ", ".join(self.PARAMETERS))
             elif action == "get":  # get wavelength
                 if (len(words) >= 2):
@@ -813,7 +813,7 @@ class AbstractCalibration(object):
                         else:
                             print("No a parameter: %s" % param)
                 else:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
 
             elif action == "set":  # set wavelength 1e-10
                 if (len(words) in (3, 4)) and words[1] in self.PARAMETERS:
@@ -830,7 +830,7 @@ class AbstractCalibration(object):
                                 scale = unit.scale
                         setattr(self.geoRef, param, value / scale)
                 else:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
             elif action == "fix":  # fix wavelength
                 if (len(words) >= 2):
                     for param in words[1:]:
@@ -840,7 +840,7 @@ class AbstractCalibration(object):
                         else:
                             print("No a parameter: %s" % param)
                 else:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
             elif action == "free":  # free wavelength
                 if (len(words) >= 2):
                     for param in words[1:]:
@@ -850,7 +850,7 @@ class AbstractCalibration(object):
                         else:
                             print("No a parameter: %s" % param)
                 else:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
 
             elif action == "recalib":
                 max_rings = None
@@ -922,9 +922,9 @@ class AbstractCalibration(object):
                             self.geoRef.__getattribute__("set_%s" % param)(value)
                             self.geoRef.__getattribute__("set_%s_max" % param)(value_max)
                     else:
-                        print(self.HELP[action])
+                        print(self._HELP[action])
                 else:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
             elif action == "bounds":
                 readFloatFromKeyboard("Enter Distance in meter "
                                       "(or dist_min[%.3f] dist[%.3f] dist_max[%.3f]):\t " %
@@ -1037,9 +1037,9 @@ class AbstractCalibration(object):
                     else:
                         print("No such parameter %s" % param)
                 else:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
             elif action == "chiplot":
-                    print(self.HELP[action])
+                    print(self._HELP[action])
                     rings = None
                     if len(words) > 1:
                         try:
@@ -1049,7 +1049,7 @@ class AbstractCalibration(object):
                     self.chiplot(rings)
             elif action == "delete":
                 if len(words) < 2:
-                    print(self.HELP[action])
+                    print(self._HELP[action])
                 else:
                     for code in words[1:]:
                         self.peakPicker.remove_grp(code)

pyFAI/gui/matplotlib.py

@@ -22,6 +22,7 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
+
 """This module inits matplotlib and setups the backend to use.
 
 It MUST be imported prior to any other import of matplotlib.
@@ -29,11 +30,12 @@ It MUST be imported prior to any other import of matplotlib.
 It provides the matplotlib :class:`FigureCanvasQTAgg` class corresponding
 to the used backend.
 """
+
 from __future__ import absolute_import
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "20/02/2018"
+__date__ = "17/05/2019"
 
 
 import sys

pyFAI/gui/model/ListModel.py

@@ -27,7 +27,7 @@ from __future__ import absolute_import
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "11/04/2019"
+__date__ = "17/05/2019"
 
 import functools
 
@@ -41,8 +41,8 @@ class ChangeEvent(object):
         """
         Define a change done on an item from the :class:`ListModel`.
 
-        :param int index, The location where to put/remove the item (before the change)
-            or the current index of the changed item
+        :param int index: The location where to put/remove the item (before the
+            change) or the current index of the changed item
         :param object item: The item involved in this change
         :param bool updated: True if the item was changed
         :param bool added: True if the item was added

pyFAI/gui/model/PeakModel.py

@@ -27,7 +27,7 @@ from __future__ import absolute_import
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "07/05/2019"
+__date__ = "17/05/2019"
 
 import numpy
 from .AbstractModel import AbstractModel
@@ -91,7 +91,7 @@ class PeakModel(AbstractModel):
 
         List of axis/ord can be reached like that.
 
-        .. code-block::
+        .. code-block:: python
 
             coords = group.coords()
             yy = coords[:, 0]

pyFAI/gui/tasks/IntegrationTask.py

@@ -27,7 +27,7 @@ from __future__ import absolute_import
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "16/05/2019"
+__date__ = "17/05/2019"
 
 import logging
 import numpy
@@ -767,8 +767,8 @@ class IntegrationPlot(qt.QFrame):
 
     def setIntegrationProcess(self, integrationProcess):
         """
-        :param IntegrationProcess integrationProcess: Result of the integration
-            process
+        :param :class:`~pyFAI.gui.tasks.IntegrationTask.IntegrationProcess` integrationProcess:
+            Result of the integration process
         """
         self.__clearRings()
 

pyFAI/gui/test/test_calibration.py

@@ -34,19 +34,14 @@ __author__ = "Valentin Valls"
 __contact__ = "valentin.valls@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "15/01/2019"
+__date__ = "16/05/2019"
 
 import unittest
 import logging
 import numpy
 
 from silx.gui import qt
-try:
-    from silx.gui.utils import testutils
-except ImportError:
-    # silx 0.8 and earlly
-    from silx.gui.test import utils as testutils
-
+from silx.gui.utils import testutils
 import pyFAI.resources
 import pyFAI.calibrant
 import pyFAI.detectors

pyFAI/gui/test/test_integrate_widget.py

@@ -34,15 +34,14 @@ __author__ = "Valentin Valls"
 __contact__ = "valentin.valls@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "25/02/2019"
+__date__ = "16/05/2019"
 
-import os
-import sys
 import unittest
 import logging
 
 from silx.gui import qt
 from ...gui.widgets.WorkerConfigurator import WorkerConfigurator
+from silx.gui.utils import testutils
 from pyFAI.test.utilstest import UtilsTest
 from pyFAI.io import integration_config
 
@@ -50,32 +49,15 @@ from pyFAI.io import integration_config
 logger = logging.getLogger(__name__)
 
 
-class TestIntegrationDialog(unittest.TestCase):
+class TestIntegrationDialog(testutils.TestCaseQt):
 
     @classmethod
     def setUpClass(cls):
-        cls.app = None
-        if sys.platform.startswith('linux') and not os.environ.get('DISPLAY', ''):
-            # On linux and no DISPLAY available (e.g., ssh without -X)
-            logger.warning('pyFAI.integrate_widget tests disabled (DISPLAY env. variable not set)')
-            cls.app = None
-        elif qt is not None:
-            cls.app = qt.QApplication([])
-
+        super(TestIntegrationDialog, cls).setUpClass()
         config = {"poni": UtilsTest.getimage("Pilatus1M.poni")}
         integration_config.normalize(config, inplace=True)
         cls.base_config = config
 
-    def setUp(self):
-        if qt is None:
-            self.skipTest("Qt is not available")
-        if self.__class__.app is None:
-            self.skipTest("DISPLAY env. is not set")
-
-    @classmethod
-    def tearDownClass(cls):
-        cls.app = None
-
     def test_config_flatdark_v1(self):
         dico = {"dark_current": "a,b,c",
                 "flat_field": "a,b,d"}

pyFAI/gui/test/test_model.py

@@ -34,18 +34,13 @@ __author__ = "Valentin Valls"
 __contact__ = "valentin.valls@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "11/04/2019"
+__date__ = "16/05/2019"
 
 import unittest
 import logging
 import numpy
 
-try:
-    from silx.gui.utils import testutils
-except ImportError:
-    # silx 0.8 and earlly
-    from silx.gui.test import utils as testutils
-
+from silx.gui.utils import testutils
 from ..model.PeakModel import PeakModel
 from ..model.ListModel import ListModel
 from ..model.DataModel import DataModel

pyFAI/gui/utils/timeutils.py

@@ -30,7 +30,7 @@ from __future__ import division
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "05/11/2018"
+__date__ = "17/05/2019"
 
 
 import logging
@@ -43,7 +43,8 @@ class Timer(object):
     """Kind of context manager to call a code while the amount of seconds is
     not finished.
 
-    .. code-block::
+    .. code-block:: python
+
         timer = Timer(seconds=10)
         while not timer.isTimeout():
             print("Tick")

pyFAI/gui/widgets/AdvancedComboBox.py

@@ -27,7 +27,7 @@ from __future__ import absolute_import
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "25/04/2019"
+__date__ = "17/05/2019"
 
 import logging
 
@@ -139,7 +139,7 @@ class AdvancedComboBox(qt.QComboBox):
 
         Only `qt.Qt.DisplayRole` and `qt.Qt.DecorationRole` are supported.
 
-        .. code-block::
+        .. code-block:: python
 
             def displayedData(widget, row, role=qt.Qt.DisplayRole):
                 if role == qt.Qt.DisplayRole:

pyFAI/gui/widgets/CalibrantPreview.py

@@ -27,7 +27,7 @@ from __future__ import absolute_import
 
 __authors__ = ["V. Valls"]
 __license__ = "MIT"
-__date__ = "10/05/2019"
+__date__ = "16/05/2019"
 
 import logging
 import numpy
@@ -55,6 +55,7 @@ class CalibrantPreview(qt.QFrame):
         self.__calibrant = None
         self.__waveLength = None
         self.__pixmap = None
+        self.__cachedSize = None
         self.setMinimumSize(qt.QSize(50, 20))
 
     def setCalibrant(self, calibrant):
@@ -103,14 +104,14 @@ class CalibrantPreview(qt.QFrame):
             fileds.append((u"Name", name, None))
         fileds.append((u"Nb registered rays", calibrant.count_registered_dSpacing(), None))
         dSpacing = calibrant.get_dSpacing()
-        fileds.append((u"Nb visible rays", len(dSpacing), u"between 0 and π"))
+        fileds.append((u"Nb visible rays", len(dSpacing), u"between 0 and 180°"))
         if len(dSpacing) > 0:
             ray = calibrant.get_dSpacing()[0]
             angle = calibrant.get_2th()[0]
-            fileds.append((u"First visible ray", u"%f (%f rad)" % (ray, angle), None))
+            fileds.append((u"First visible ray", u"%f Å (%f°)" % (ray, numpy.rad2deg(angle)), None))
             ray = calibrant.get_dSpacing()[-1]
             angle = calibrant.get_2th()[-1]
-            fileds.append((u"Last visible ray", u"%f (%f rad)" % (ray, angle), None))
+            fileds.append((u"Last visible ray", u"%f Å (%f°)" % (ray, numpy.rad2deg(angle)), None))
 
         toolTip = []
         for f in fileds:
@@ -124,31 +125,23 @@ class CalibrantPreview(qt.QFrame):
         toolTip = u"<html><ul>%s</ul></html>" % toolTip
         self.setToolTip(toolTip)
 
-    def __getPixmap(self):
-        if self.__pixmap is not None:
+    def __getPixmap(self, size=360):
+        if self.__pixmap is not None and self.__cachedSize == size:
             return self.__pixmap
-
         calibrant = self.__getConfiguredCalibrant()
         if calibrant is None:
             return None
         tths = numpy.array(calibrant.get_2th())
 
         tth_min, tth_max = 0, numpy.pi
-        size = 360
-        agregation = numpy.zeros((1, size))
-        for tth in tths:
-            pos = int((tth - tth_min) / (tth_max - tth_min) * size)
-            if pos < 0:
-                continue
-            if pos >= size:
-                continue
-            agregation[0, pos] += 1
-
+        histo = numpy.histogram(tths, bins=size, range=(tth_min, tth_max))
+        agregation = histo[0].reshape(1, -1)
         colormap = Colormap(name="reversed gray", vmin=agregation.min(), vmax=agregation.max())
         rgbImage = colormap.applyToData(agregation)[:, :, :3]
         qimage = imageutils.convertArrayToQImage(rgbImage)
         qpixmap = qt.QPixmap.fromImage(qimage)
         self.__pixmap = qpixmap
+        self.__cachedSize = size
         return self.__pixmap
 
     def paintEvent(self, event):
@@ -167,9 +160,9 @@ class CalibrantPreview(qt.QFrame):
                           self)
 
         # content
-        pixmap = self.__getPixmap()
         pixmapRect = self.rect().adjusted(self._PIXMAP_OFFSET, self._PIXMAP_OFFSET,
                                           -self._PIXMAP_OFFSET, -self._PIXMAP_OFFSET)
+        pixmap = self.__getPixmap(size=pixmapRect.width())
         if pixmap is not None:
             painter.drawPixmap(pixmapRect,
                                pixmap,

pyFAI/opencl/__init__.py

@@ -30,11 +30,13 @@
 # OTHER DEALINGS IN THE SOFTWARE.
 #
 
+"""Contains all OpenCL implementation."""
+
 __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "2012-2017 European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "25/02/2019"
+__date__ = "17/05/2019"
 __status__ = "stable"
 
 import os

pyFAI/opencl/azim_csr.py

@@ -29,14 +29,14 @@
 
 __authors__ = ["Jérôme Kieffer", "Giannis Ashiotis"]
 __license__ = "MIT"
-__date__ = "11/01/2019"
+__date__ = "16/05/2019"
 __copyright__ = "2014-2017, ESRF, Grenoble"
 __contact__ = "jerome.kieffer@esrf.fr"
 
 import logging
 from collections import OrderedDict
 import numpy
-from . import pyopencl, kernel_workgroup_size
+from . import pyopencl
 from ..utils import calc_checksum
 
 if pyopencl:
@@ -46,6 +46,7 @@ else:
 
 from . import processing
 from . import get_x87_volatile_option
+from . import kernel_workgroup_size
 EventDescription = processing.EventDescription
 OpenclProcessing = processing.OpenclProcessing
 BufferDescription = processing.BufferDescription

pyFAI/opencl/ocl_hist_pixelsplit.py

@@ -30,7 +30,7 @@
 
 __authors__ = ["Jérôme Kieffer", "Giannis Ashiotis"]
 __license__ = "MIT"
-__date__ = "06/05/2019"
+__date__ = "16/05/2019"
 __copyright__ = "2014, ESRF, Grenoble"
 __contact__ = "jerome.kieffer@esrf.fr"
 
@@ -42,8 +42,7 @@ from . import ocl
 if ocl is not None:
     from . import pyopencl, allocate_cl_buffers, release_cl_buffers
     mf = pyopencl.mem_flags
-from ..ext.splitBBoxLUT import HistoBBox1d
-from . import utils
+    from . import concatenate_cl_kernel
 from ..utils import crc32
 
 logger = logging.getLogger(__name__)
@@ -200,7 +199,7 @@ class OCL_Hist_Pixelsplit(object):
         :param kernel_file: path tothe
         """
         kernel_file = kernel_file or "ocl_hist_pixelsplit.cl"
-        kernel_src = utils.concatenate_cl_kernel([kernel_file])
+        kernel_src = concatenate_cl_kernel([kernel_file])
 
         template_options = "-D BINS=%i  -D NIMAGE=%i -D WORKGROUP_SIZE=%i -D EPS=%f"
         compile_options = template_options % (self.bins, self.size, self.BLOCK_SIZE, numpy.finfo(numpy.float32).eps)

pyFAI/opencl/preproc.py

@@ -33,7 +33,7 @@ from __future__ import absolute_import, print_function, division
 
 __author__ = "Jérôme Kieffer"
 __license__ = "MIT"
-__date__ = "15/03/2019"
+__date__ = "16/05/2019"
 __copyright__ = "2015-2017, ESRF, Grenoble"
 __contact__ = "jerome.kieffer@esrf.fr"
 
@@ -42,7 +42,10 @@ logger = logging.getLogger(__name__)
 
 from collections import OrderedDict
 import numpy
-from . import pyopencl, mf, processing
+from . import pyopencl
+if pyopencl is None:
+    raise ImportError("pyopencl is not installed")
+from . import mf, processing
 EventDescription = processing.EventDescription
 OpenclProcessing = processing.OpenclProcessing
 BufferDescription = processing.BufferDescription

pyFAI/opencl/sort.py

@@ -35,7 +35,7 @@ from __future__ import absolute_import, print_function, division
 
 __author__ = "Jérôme Kieffer"
 __license__ = "MIT"
-__date__ = "11/01/2019"
+__date__ = "16/05/2019"
 __copyright__ = "2015, ESRF, Grenoble"
 __contact__ = "jerome.kieffer@esrf.fr"
 
@@ -44,7 +44,7 @@ import logging
 logger = logging.getLogger(__name__)
 from collections import OrderedDict
 import numpy
-from . import ocl, release_cl_buffers, kernel_workgroup_size, get_x87_volatile_option
+from . import ocl
 if ocl:
     import pyopencl.array
     from . import processing
@@ -53,6 +53,7 @@ if ocl:
     BufferDescription = processing.BufferDescription
 else:
     raise ImportError("pyopencl is not installed or no device is available")
+from. import release_cl_buffers, kernel_workgroup_size, get_x87_volatile_option
 
 
 class Separator(OpenclProcessing):

pyFAI/resources/__init__.py

@@ -34,26 +34,29 @@ of this modules to ensure access across different distribution schemes:
 - Frozen fat binary application using pyFAI (frozen with cx_Freeze or py2app).
   This needs special care for the resource files in the setup:
 
-  - With cx_Freeze, add pyFAI/resources to include_files::
+- With cx_Freeze, add pyFAI/resources to include_files:
+
+.. code-block:: python
 
     import pyFAI.resources
     pyFAI_include_files = (os.path.dirname(pyFAI.resources.__file__),
                           os.path.join('pyFAI', 'resources'))
-    setup(...
-          options={'build_exe': {'include_files': [pyFAI_include_files]}}
-          )
+    setup(...,
+        options={'build_exe': {'include_files': [pyFAI_include_files]}}
+    )
 
+- With py2app, add pyFAI in the packages list of the py2app options:
 
-  - With py2app, add pyFAI in the packages list of the py2app options::
+.. code-block:: python
 
-    setup(...
-          options={'py2app': {'packages': ['pyFAI']}}
-          )
+    setup(...,
+        options={'py2app': {'packages': ['pyFAI']}}
+    )
 """
 
 __authors__ = ["V.A. Sole", "Thomas Vincent"]
 __license__ = "MIT"
-__date__ = "20/02/2018"
+__date__ = "17/05/2019"
 
 
 import os

pyFAI/test/test_bug_regression.py

@@ -39,7 +39,7 @@ __author__ = "Jérôme Kieffer"
 __contact__ = "Jerome.Kieffer@esrf.fr"
 __license__ = "MIT"
 __copyright__ = "2015-2018 European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "11/12/2018"
+__date__ = "16/05/2019"
 
 import sys
 import os
@@ -226,44 +226,64 @@ class TestBugRegression(unittest.TestCase):
         hc = 12.398419292004204  # Old reference value
         self.assertAlmostEqual(hc, units.hc, 6, "hc is correct, got %s" % units.hc)
 
-    def test_bug_808(self):
+    def test_import_all_modules(self):
         """Try to import every single module in the package
         """
         import pyFAI
-#         print(pyFAI.__file__)
-#         print(pyFAI.__name__)
         pyFAI_root = os.path.split(pyFAI.__file__)[0]
 
+        def must_be_skipped(path):
+            path = os.path.relpath(path, pyFAI_root)
+            path = path.replace("\\", "/")
+            elements = path.split("/")
+            if "test" in elements:
+                # Always skip test modules
+                logger.warning("Skip test module %s", path)
+                return True
+            if not UtilsTest.WITH_OPENCL_TEST:
+                if "opencl" in elements:
+                    logger.warning("Skip %s. OpenCL tests disabled", path)
+                    return True
+            if not UtilsTest.WITH_QT_TEST:
+                if "gui" in elements:
+                    logger.warning("Skip %s. Qt tests disabled", path)
+                    return True
+            return False
+
         for root, dirs, files in os.walk(pyFAI_root, topdown=True):
             for adir in dirs:
-
                 subpackage_path = os.path.join(root, adir, "__init__.py")
+                if must_be_skipped(subpackage_path):
+                    continue
                 subpackage = "pyFAI" + subpackage_path[len(pyFAI_root):-12].replace(os.sep, ".")
                 if os.path.isdir(subpackage_path):
                     logger.info("Loading subpackage: %s from %s", subpackage, subpackage_path)
                     sys.modules[subpackage] = load_source(subpackage, subpackage_path)
             for name in files:
-                if name.endswith(".py"):
-                    path = os.path.join(root, name)
-                    fqn = "pyFAI" + path[len(pyFAI_root):-3].replace(os.sep, ".")
-                    logger.info("Importing %s from %s", fqn, path)
-                    try:
-                        load_source(fqn, path)
-                    except Exception as err:
-                        if ((isinstance(err, ImportError) and
-                                "No Qt wrapper found" in err.__str__() or
-                                "pyopencl is not installed" in err.__str__() or
-                                "PySide" in err.__str__()) or
-                            (isinstance(err, SystemError) and
-                                "Parent module" in err.__str__())):
+                if not name.endswith(".py"):
+                    continue
+                path = os.path.join(root, name)
+                if must_be_skipped(path):
+                    continue
+                fqn = "pyFAI" + path[len(pyFAI_root):-3].replace(os.sep, ".")
+                logger.info("Importing %s from %s", fqn, path)
+                try:
+                    load_source(fqn, path)
+                except Exception as err:
+                    if ((isinstance(err, ImportError) and
+                            "No Qt wrapper found" in err.__str__() or
+                            "pyopencl is not installed" in err.__str__() or
+                            "PySide" in err.__str__()) or
+                        (isinstance(err, SystemError) and
+                            "Parent module" in err.__str__())):
 
-                            logger.info("Expected failure importing %s from %s with error: %s",
-                                        fqn, path, err)
-                        else:
-                            logger.error("Failed importing %s from %s with error: %s%s: %s",
-                                         fqn, path, os.linesep,
-                                         err.__class__.__name__, err)
-                            raise err
+                        logger.info("Expected failure importing %s from %s with error: %s",
+                                    fqn, path, err)
+                    else:
+                        logger.error("Failed importing %s from %s with error: %s%s: %s",
+                                     fqn, path, os.linesep,
+                                     err.__class__.__name__, err)
+                        raise err
 
     def test_bug_816(self):
         "Ensure the chi-disontinuity is properly set"

pyFAI/test/test_detector.py

@@ -33,7 +33,7 @@ __author__ = "Picca Frédéric-Emmanuel, Jérôme Kieffer",
 __contact__ = "picca@synchrotron-soleil.fr"
 __license__ = "MIT+"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "01/03/2019"
+__date__ = "16/05/2019"
 
 import os
 import tempfile
@@ -169,7 +169,7 @@ class TestDetector(unittest.TestCase):
             if os.path.exists(fname):  # already tested with another alias
                 continue
             det = detector_factory(det_name)
-            logger.info("%s --> nxs", det_name)
+            logger.debug("%s --> nxs", det_name)
             if (det.pixel1 is None) or (det.shape is None):
                 continue
             if (det.shape[0] > 1900) or (det.shape[1] > 1900):

pyFAI/test/test_preproc.py

@@ -151,9 +151,10 @@ class TestPreproc(unittest.TestCase):
 
     @unittest.skipIf(UtilsTest.opencl is False, "User request to skip OpenCL tests")
     def test_opencl(self):
-        from ..opencl import ocl, preproc as ocl_preproc
+        from ..opencl import ocl
         if ocl is None:
             self.skipTest("OpenCL not available")
+        from ..opencl import preproc as ocl_preproc
         self.one_test(ocl_preproc)
 
 

pyFAI/units.py

@@ -205,7 +205,7 @@ register_radial_unit("q_A^-1",
                      label=r"Scattering vector $q$ ($\AA^{-1}$)",
                      equation=eq_q,
                      short_name="q",
-                     unit_symbol="\AA^{-1}")
+                     unit_symbol=r"\AA^{-1}")
 
 register_radial_unit("d*2_A^-2",
                      center="rd2Array",
@@ -214,7 +214,7 @@ register_radial_unit("d*2_A^-2",
                      label=r"Reciprocal spacing squared $d^{*2}$ ($\AA^{-2}$)",
                      equation=lambda x, y, z, wavelength: (eq_q(x, y, z, wavelength) / (2.0 * numpy.pi)) ** 2,
                      short_name="d^{*2}",
-                     unit_symbol="\AA^{-2}")
+                     unit_symbol=r"\AA^{-2}")
 
 register_radial_unit("d*2_nm^-2",
                      center="rd2Array",

pyFAI/utils/__init__.py

@@ -27,14 +27,14 @@
 #  THE SOFTWARE.
 
 """
-Utilities
+Module with miscelaneous tools
 """
 
 __author__ = "Jerome Kieffer"
 __contact__ = "Jerome.Kieffer@ESRF.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "04/10/2018"
+__date__ = "17/05/2019"
 __status__ = "production"
 
 import logging

pyFAI/utils/bayes.py

@@ -23,11 +23,12 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
-""" Bayesian evaluation of background for 1D powder diffraction pattern
+"""Bayesian evaluation of background for 1D powder diffraction pattern.
 
 Code according to Sivia and David, J. Appl. Cryst. (2001). 34, 318-324
-# Version: 0.1 2012/03/28
-# Version: 0.2 2016/10/07: OOP implementation
+
+* Version: 0.1 2012/03/28
+* Version: 0.2 2016/10/07: OOP implementation
 """
 
 from __future__ import absolute_import, print_function, division
@@ -35,7 +36,7 @@ from __future__ import absolute_import, print_function, division
 __authors__ = ["Vincent Favre-Nicolin", "Jérôme Kieffer"]
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "09/01/2018"
+__date__ = "17/05/2019"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 
@@ -53,7 +54,7 @@ class BayesianBackground(object):
 
     .. math:: z =  y / sigma^2
 
-    * if z<0: a quadratic behaviour is expected
+    * if z<0 a quadratic behaviour is expected
     * if z>>1 it is likely a bragg peak so the penalty should be small: log(z).
     * The spline is used to have a quadratic behaviour near 0 and the log one
       near the junction
@@ -126,9 +127,11 @@ class BayesianBackground(object):
     def bayes_llk(cls, z):
         """Calculate actually the log-likelihood from a set of weighted error
 
-        Re implementation of:
-        (y<=0)*5*y**2 + (y>0)*(y<8)*pyFAI.utils.bayes.background.spline(y) + (y>=8)*(s1+log(abs(y)+1*(y<8)))
-        even slightly faster
+        Re implementation of the following code even slightly faster:
+
+        .. code-block:: python
+
+            (y<=0)*5*y**2 + (y>0)*(y<8)*pyFAI.utils.bayes.background.spline(y) + (y>=8)*(s1+log(abs(y)+1*(y<8)))
 
         :param float[:] z: weighted error
         :return: log likelihood

pyFAI/utils/mathutil.py

@@ -736,10 +736,7 @@ def is_far_from_group(pt, lst_pts, d2):
 
 
 def rwp(obt, ref):
-    """          ___________________________
-    Calculate  \/     4 ( obt - ref)²
-               V Sum( --------------- )
-                        (obt + ref)²
+    """Compute :math:`\\sqrt{\\sum \\frac{4\\cdot(obt-ref)^2}{(obt + ref)^2}}`.
 
     This is done for symmetry reason between obt and ref
 

pyFAI/utils/shell.py

@@ -23,14 +23,14 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 
-"""Module containing utilities around shell"""
+"""Module containing utilities around shell command line."""
 
 from __future__ import absolute_import, print_function, division
 
 __author__ = "valentin.valls@esrf.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "25/02/2019"
+__date__ = "17/05/2019"
 __status__ = "development"
 __docformat__ = 'restructuredtext'
 

pyFAI/utils/stringutil.py

@@ -26,12 +26,12 @@
 
 from __future__ import absolute_import, print_function, division
 
-"""Module containing utilitary around string"""
+"""Module containing enhanced string formatters."""
 
 __author__ = "valentin.valls@esrf.eu"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "16/05/2019"
+__date__ = "17/05/2019"
 __status__ = "development"
 __docformat__ = 'restructuredtext'