xi-cam / xi-cam.saxs Goto Github PK

1.0 1.0 7.0 552 KB

The (GI-)SAXS/WAXS plugin for Xi-CAM.

License: BSD 3-Clause "New" or "Revised" License

Python 100.00%

xi-cam.saxs's Introduction

Xi-CAM

Xi-cam is a graphical environment for synchrotron data analysis, management, and visualization developed by the Advanced Light Source at Lawrence Berkeley National Laboratory. This is a cross-platform open-source Python 3 project licensed under BSD.

Installation

The latest stable Xi-CAM is available on pypi

pip install xicam

For more information, see the installation documentation.

Resources

Documentation: https://xi-cam.readthedocs.io/en/latest
Report an issue in Xi-CAM: New Bug Report

xi-cam.saxs's People

Contributors

Stargazers

Watchers

Forkers

tacaswell gfreychet ihumphrey richardk2n julreinhardt tangkong huyuhuster

xi-cam.saxs's Issues

Results tree default naming needs more information

Currently, the value shown for a 1-Time correlation is 1-Time Correlation. This should at least show the scanid tacked on.

We may need to re-review what we information we are storing with the workflow and how to appropriately display this information (e.g. what are the values of the parameters for this workflow's execution, what roi was used, etc.)?

Potentially, representing this tree with extra columns for this information (scanid, date, name, roi, etc) could be useful as well (which could hook into Qt's filtering and sorting nicely) (consider adding this as a separate issue if we want this).

Create projections for SAXS (remove injected schema code)

Should ROIs be created for all views? (ROI management)

Currently an ROI is created for the active view, but not shared among any other open views.

This may require some thought about how we manage ROIs in general. Do we want a widget that allows for managing ROIs (hiding/showing ROIs, deleting ROIs, naming ROIs, creating ROIs, etc.)? How would we internally manage ROIs? How would this design fit with the way ROIs are currently being inserted into a workflow?

Add context menu to the results tree

This context menu could allow:

renaming a result
removing a result
...

Improve peak order identification in naive sdd (add UI for override)

Restore SAXS Calibration Panel

Fit projectors into GUIPlugins stage-mixin based design

Ewald Sphere correction

Cake Mode as mixin

Add intents to SAXS operations

Programmatic ROI definition

Currently, ROI definition in the XPCS plugin is performed with a GUI. From the CSX beamline, we have gotten feedback where there are cases where they would like to programmatically define ROIs. This would provide ease of use when creating multiple ROIs and allow for more precise definitions of the ROIs.

Segmeneted Arc ROI

Fix camsaxs remeshing

Teach SAXS to use ensemblemodel

Masking operations

Write projections which return intents

Implement Compare stage

single-source project version

helps with distributions

Saving workflow to reapply to future scans

Currently in the XPCS plugin (to be merged into the SAXS plugin), processing workflow steps are statically defined. The user has the ability to modify parameters. There is not currently functionality to save those parameters and use them again in future analyses.

The CSX beamline would like the ability to save workflows and/or parameters across analyses of run. This needs to be thought out a bit with Xi-Cam's framework. Much of this functionality might be more natural with the integration of camlink2 within Xi-Cam. Howesver, it might be feasible to take some intermediate steps like saving parameters across scans and possibly saving those settings in QSettings so that they are re-constituted when Xi-Cam is closed an reopened.

Interpret SAXSImageIntent in SAXSImageCanvas

Move HintTabView into gui

HintTabView could be moved into gui instead of living in SAXS

Update SAXS/XPCS ingestors to returnlist of intents

Put astroscrappy as an optional package for the SAXS plugin

Fix camsaxs setup.py

UI for detectormask op

Aggregate example test data of various formats

edf
nxcansas
tif
fits
...


/home/beams10/8IDIUSER/src/Xi-cam.core/xicam/core/msg/__init__.py:213: UserWarning: Custom loggername is no longer supported, ignored.
  warnings.warn("Custom loggername is no longer supported, "
Thu Feb 06 11:00:02 2020 - logError - ERROR - MainThread - 
 The following error was handled safely by Xi-cam. It is displayed here for debugging.
Thu Feb 06 11:00:02 2020 - logError - ERROR - MainThread - 
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 186, in dataChanged
    self.addDevice(field)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 100, in setSilence
    self.save()
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/xicam/plugins/settingsplugin.py", line 45, in save
    QSettings().setValue(self.name(), pickle.dumps(self.toState()))
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/cloudpickle/cloudpickle_fast.py", line 62, in dumps
    cp.dump(obj)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/cloudpickle/cloudpickle_fast.py", line 538, in dump
    return Pickler.dump(self, obj)
 TypeError: cannot pickle 'property' object
Thu Feb 06 11:00:02 2020 - run - ERROR - Dummy-22 - Error in thread: Method: doReduceWorkflow
Args: (<xicam.SAXS.SAXSGUIPlugin.SAXSPlugin object at 0x7fd728d9ed90>,)
Kwargs: {}
Thu Feb 06 11:00:02 2020 - logError - ERROR - Dummy-22 - 
 The following error was handled safely by Xi-cam. It is displayed here for debugging.
Thu Feb 06 11:00:02 2020 - logError - ERROR - Dummy-22 - 
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 160, in addDevice
    self.addChild(devicechild)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 497, in addChild
    return self.insertChild(len(self.childs), child, autoIncrementName=autoIncrementName)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/pyqtgraph/parametertree/Parameter.py", line 540, in insertChild
    raise Exception("Already have child named %s" % str(name))
 Exception: Already have child named lambdadet_image
 
During handling of the above exception, another exception occurred:
 Traceback (most recent call last):
   File "/home/beams10/8IDIUSER/src/Xi-cam.core/xicam/core/threads/__init__.py", line 151, in run
    for self._result in self._run(*args, **kwargs):
   File "/home/beams10/8IDIUSER/src/Xi-cam.core/xicam/core/threads/__init__.py", line 176, in _run
    yield self.method(*self.args, **self.kwargs)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/SAXSGUIPlugin.py", line 466, in doReduceWorkflow
    ai = self.calibrationsettings.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 98, in setSilence
    self.emitChanges()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 90, in emitChanges
    self.genAIs()
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 113, in genAIs
    ai = self.AI(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 129, in AI
    self.addDevice(device)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 166, in addDevice
    self.setSilence(False)
   File "/home/beams10/8IDIUSER/src/Xi-cam.SAXS/xicam/SAXS/calibration/__init__.py", line 100, in setSilence
    self.save()
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/xicam/plugins/settingsplugin.py", line 45, in save
    QSettings().setValue(self.name(), pickle.dumps(self.toState()))
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/cloudpickle/cloudpickle_fast.py", line 62, in dumps
    cp.dump(obj)
   File "/home/beams/8IDIUSER/.conda/envs/xicam-pilot/lib/python3.8/site-packages/cloudpickle/cloudpickle_fast.py", line 538, in dump
    return Pickler.dump(self, obj)
 TypeError: cannot pickle 'property' object

implement CI / auto deploys to testpypi

It would be helpful to have CI (travis or github actions) set up for this to automatically deploy to xicam.SAXS at testpypi.

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