mirror of https://github.com/silx-kit/pyFAI.git
Merge remote-tracking branch 'upstream/master' into 0.18
This commit is contained in:
Jerome Kieffer
commit
cc694e178a
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@ -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:
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
pyFAI.detectors package
|
||||
=======================
|
||||
|
||||
Module contents
|
||||
---------------
|
||||
|
||||
.. automodule:: pyFAI.detectors
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
@ -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:
|
||||
|
|
@ -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
|
||||
|
|
|
|||
Binary file not shown.
|
Before Width: | Height: | Size: 82 KiB After Width: | Height: | Size: 66 KiB |
|
|
@ -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
|
||||
-------------
|
||||
|
|
|
|||
|
|
@ -1,6 +1,8 @@
|
|||
Mask generation tool: pyFAI-drawmask
|
||||
====================================
|
||||
|
||||
.. _pyFAI-drawmask:
|
||||
|
||||
Purpose
|
||||
-------
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
----------------------
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
@ -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.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
<?xml version="1.0" encoding="UTF-8" standalone="no"?><umlet_diagram></umlet_diagram>
|
||||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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]
|
||||
|
|
|
|||
|
|
@ -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()
|
||||
|
||||
|
|
|
|||
|
|
@ -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")
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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'
|
||||
|
||||
|
|
|
|||
|
|
@ -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'
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue