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Plugin link #6

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merged 2 commits into from
Dec 5, 2019
Merged

Plugin link #6

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88d3f12
New version of XPCS plugin as a link to SAXS stages
ronpandolfi Nov 23, 2019
6669857
Add method redirects for XPCS/SAXS
ronpandolfi Nov 27, 2019
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1 change: 0 additions & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ scipy
scikit-image
xicam.SAXS
event-model
intake_bluesky

# Wait until ronpandolfi's changes (#542) are in release /PyPi ...
scikit-beam @ git+https://github.com/scikit-beam/scikit-beam
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3 changes: 1 addition & 2 deletions setup.py
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Expand Up @@ -39,6 +39,5 @@
install_requires=install_requires,
#dependency_links=dependency_links,
author_email='ronpandolfi@lbl.gov',
entry_points={'xicam.plugins.GUIPlugin': ['xpcs_gui_plugin = xicam.XPCS:XPCS'],
'xicam.plugins.CatalogPlugin': ['aps_xpcs = xicam.XPCS.formats.APSXPCS:APSXPCS']},
entry_points={'xicam.plugins.GUIPlugin': ['xpcs_gui_plugin = xicam.XPCS:XPCS'], },
)
309 changes: 5 additions & 304 deletions xicam/XPCS/__init__.py
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@@ -1,313 +1,14 @@
import pathlib
import time
from functools import partial

import cloudpickle as pickle
import event_model
from databroker.core import BlueskyRun
from pyqtgraph.parametertree import Parameter, ParameterTree
from pyqtgraph.parametertree.parameterTypes import ListParameter
from qtpy.QtCore import *
from qtpy.QtGui import *
from qtpy.QtWidgets import *

from xicam.core import msg
from xicam.core.data import NonDBHeader
from xicam.gui import static
from xicam.gui.widgets.imageviewmixins import PolygonROI
from xicam.gui.widgets.ROI import BetterROI
from xicam.gui.widgets.tabview import TabView
from xicam.plugins import GUILayout, GUIPlugin
from xicam.plugins import manager as pluginmanager
from xicam.SAXS.widgets.SAXSViewerPlugin import SAXSViewerPluginBase

from .widgets.views import CorrelationWidget, FileSelectionView, OneTimeWidget, TwoTimeWidget
from .workflows import FourierAutocorrelator, OneTime, TwoTime


class BlueskyItem(QStandardItem):

def __init__(self):
super(QStandardItem, self).__init__()


class XPCSViewerPlugin(PolygonROI, SAXSViewerPluginBase):
pass


class XPCSProcessor(ParameterTree):
def __init__(self, *args, **kwargs):
super(XPCSProcessor, self).__init__()
self._paramName = 'Algorithm'
self._name = 'XPCS Processor'
self.workflow = None
self.param = None
self._workflows = dict()

self.listParameter = ListParameter(name=self._paramName,
values={'':''},
value='')

self.param = Parameter(children=[self.listParameter], name=self._name)
self.setParameters(self.param, showTop=False)

def update(self, *_):
for child in self.param.childs[1:]:
child.remove()

self.workflow = self._workflows.get(self.listParameter.value().name, self.listParameter.value()())
self._workflows[self.workflow.name] = self.workflow
for process in self.workflow.processes:
self.param.addChild(process.parameter)


class OneTimeProcessor(XPCSProcessor):
def __init__(self, *args, **kwargs):
super(OneTimeProcessor, self).__init__()
self._name = '1-Time Processor'
self.listParameter.setLimits(OneTimeAlgorithms.algorithms())
self.listParameter.setValue(OneTimeAlgorithms.algorithms()[OneTimeAlgorithms.default()])

self.update()
self.listParameter.sigValueChanged.connect(self.update)


class TwoTimeProcessor(XPCSProcessor):
def __init__(self, *args, **kwargs):
super(TwoTimeProcessor, self).__init__()
self._name = '2-Time Processor'
self.listParameter.setLimits(TwoTimeAlgorithms.algorithms())
self.listParameter.setValue(TwoTimeAlgorithms.algorithms()[TwoTimeAlgorithms.default()])

self.update()
self.listParameter.sigValueChanged.connect(self.update)


class ProcessingAlgorithms:
"""
Convenience class to get the available algorithms that can be used for
one-time and two-time correlations.
"""
@staticmethod
def algorithms():
return {
TwoTimeAlgorithms.name: TwoTimeAlgorithms.algorithms(),
OneTimeAlgorithms.name: OneTimeAlgorithms.algorithms()
}


class TwoTimeAlgorithms(ProcessingAlgorithms):
name = '2-Time Algorithms'
@staticmethod
def algorithms():
return {TwoTime.name: TwoTime}

@staticmethod
def default():
return TwoTime.name


class OneTimeAlgorithms(ProcessingAlgorithms):
name = '1-Time Algorithms'
@staticmethod
def algorithms():
return {OneTime.name: OneTime,
FourierAutocorrelator.name: FourierAutocorrelator}

@staticmethod
def default():
return OneTime.name

from xicam.plugins import GUILayout, GUIPlugin, manager as pluginmanager

class XPCS(GUIPlugin):
name = 'XPCS'

def __init__(self):
# XPCS data model
self.resultsModel = QStandardItemModel()

# Input (raw) data model
self.headerModel = QStandardItemModel()
self.selectionModel = QItemSelectionModel(self.headerModel)

# Widgets
self.calibrationSettings = pluginmanager.getPluginByName('xicam.SAXS.calibration',
'SettingsPlugin').plugin_object

# Setup TabViews
self.rawTabView = TabView(self.headerModel,
widgetcls=XPCSViewerPlugin,
selectionmodel=self.selectionModel,
bindings=[(self.calibrationSettings.sigGeometryChanged, 'setGeometry')],
geometry=self.getAI)

# Setup correlation views
self.twoTimeView = TwoTimeWidget()
self.twoTimeFileSelection = FileSelectionView(self.headerModel, self.selectionModel)
self.twoTimeProcessor = TwoTimeProcessor()
self.twoTimeToolBar = QToolBar()
self.twoTimeToolBar.addAction(QIcon(static.path('icons/run.png')), 'Process', self.processTwoTime)
self.twoTimeToolBar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
saxsplugin = pluginmanager.getPluginByName('SAXS', 'GUIPlugin').plugin_object

self.oneTimeView = OneTimeWidget()
self.oneTimeFileSelection = FileSelectionView(self.headerModel, self.selectionModel)
self.oneTimeProcessor = OneTimeProcessor()
self.oneTimeToolBar = QToolBar()
self.oneTimeToolBar.addAction(QIcon(static.path('icons/run.png')), 'Process', self.processOneTime)
self.oneTimeToolBar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon)
self.stages = saxsplugin.stages['Correlate']

# self.placeholder = QLabel('correlation parameters')

self.stages = {'Raw': GUILayout(self.rawTabView,
right=self.calibrationSettings.widget),
'2-Time Correlation': GUILayout(self.twoTimeView,
top=self.twoTimeToolBar,
right=self.twoTimeFileSelection,
rightbottom=self.twoTimeProcessor,),
# bottom=self.placeholder),
'1-Time Correlation': GUILayout(self.oneTimeView,
top=self.oneTimeToolBar,
right=self.oneTimeFileSelection,
rightbottom=self.oneTimeProcessor,)
# bottom=self.placeholder)
}

# TODO -- improve result caching
self._results = []
self.appendCatalog = saxsplugin.appendCatalog
self.appendHeader = saxsplugin.appendHeader

super(XPCS, self).__init__()

def appendHeader(self, header: NonDBHeader, **kwargs):
item = QStandardItem(header.startdoc.get('sample_name', '????'))
item.header = header
self.headerModel.appendRow(item)
self.selectionModel.reset()
self.selectionModel.setCurrentIndex(self.headerModel.index(self.headerModel.rowCount() - 1, 0),
QItemSelectionModel.Rows)
self.headerModel.dataChanged.emit(QModelIndex(), QModelIndex())

# Load any reduced (processed) data
reduced = False
for descriptor in header.descriptordocs:
if descriptor['name'] == '1-Time':
reduced = True
break
paths = header.startdoc.get('paths')
for path in paths:
if reduced:
startItem = QStandardItem(header.startdoc.get('sample_name', '??'))
eventlist = header.eventdocs
for event in eventlist:
eventItem = QStandardItem(repr(event['data']['dqlist']))
eventItem.setData(event, Qt.UserRole)
eventItem.setCheckable(True)
startItem.appendRow(eventItem)
# TODO -- properly add to view (one-time or 2-time, etc.)
self.oneTimeView.model.invisibleRootItem().appendRow(startItem)

def appendCatalog(self, catalog: BlueskyRun, **kwargs):
displayName = ""
if 'sample_name' in catalog.metadata['start']:
displayName = catalog.metadata['start']['sample_name']
elif 'scan_id' in catalog.metadata['start']:
displayName = catalog.metadata['start']['scan_id']
else:
displayName = catalog.metadata['start']['uid']

item = BlueskyItem(displayName)
item.setData(catalog, Qt.UserRole)
self.catalogModel.appendRow(item)
self.catalogModel.dataChanged.emit(item.index(), item.index())

def getAI(self):
return None

def currentheader(self):
return self.headerModel.itemFromIndex(self.selectionModel.currentIndex()).header

def currentheaders(self):
selected_indices = self.selectionModel.selectedIndexes()
headers = []
for model_index in selected_indices:
headers.append(self.headerModel.itemFromIndex(model_index).header)
return headers

def processOneTime(self):
canvas = self.oneTimeView.plot
canvases = dict() # Intentionally empty; unused in PlotHint
self.process(self.oneTimeProcessor,
callback_slot=partial(self.saveResult, fileSelectionView=self.oneTimeFileSelection),
finished_slot=partial(self.updateDerivedDataModel,
view=self.oneTimeView,
canvas=canvas,
canvases=canvases))

def processTwoTime(self):
canvas = None # Intentionally empty; unused in ImageHint
canvases = {"imageview": self.twoTimeView.image}
self.process(self.twoTimeProcessor,
callback_slot=partial(self.saveResult, fileSelectionView=self.twoTimeFileSelection),
finished_slot=partial(self.updateDerivedDataModel,
view=self.twoTimeView,
canvas=canvas,
canvases=canvases))

def process(self, processor: XPCSProcessor, **kwargs):
if processor:
workflow = processor.workflow

data = [header.meta_array() for header in self.currentheaders()]
currentWidget = self.rawTabView.currentWidget()
rois = [item for item in currentWidget.view.items if isinstance(item, BetterROI)]
labels = [currentWidget.poly_mask()] * len(data) # TODO: update for multiple ROIs
numLevels = [1] * len(data)

numBufs = []
for i, _ in enumerate(data):
shape = data[i].shape[0]
# multi_tau_corr requires num_bufs to be even
if shape % 2:
shape += 1
numBufs.append(shape)

if kwargs.get('callback_slot'):
callbackSlot = kwargs['callback_slot']
else:
callbackSlot = self.saveResult
if kwargs.get('finished_slot'):
finishedSlot = kwargs['finished_slot']
else:
finishedSlot = self.updateDerivedDataModel

workflowPickle = pickle.dumps(workflow)
workflow.execute_all(None,
data=data,
labels=labels,
num_levels=numLevels,
num_bufs=numBufs,
callback_slot=callbackSlot,
finished_slot=partial(finishedSlot,
header=self.currentheader(),
roi=rois[0], # todo -- handle multiple rois
workflow=workflow,
workflow_pickle=workflowPickle))

def saveResult(self, result, fileSelectionView=None):
if fileSelectionView:
analyzed_results = dict()

if not fileSelectionView.correlationName.displayText():
analyzed_results['result_name'] = fileSelectionView.correlationName.placeholderText()
else:
analyzed_results['result_name'] = fileSelectionView.correlationName.displayText()
analyzed_results = {**analyzed_results, **result}

self._results.append(analyzed_results)

def updateDerivedDataModel(self, view: CorrelationWidget, canvas, canvases, header, roi, workflow, workflow_pickle):
parentItem = BlueskyItem(workflow.name)
for hint in workflow.hints:
item = BlueskyItem(hint.name)
item.setData(hint)
item.setCheckable(True)
parentItem.appendRow(item)
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