Merge pull request #3 from nanthony21/dev

Dev

conda.recipe/meta.yaml

@@ -32,9 +32,10 @@ requirements:
     - google-auth-httplib2
     - google-auth-oauthlib
     - pyqt =5
-    - pwspy >=0.2.3 # Core pws package, available on backmanlab anaconda cloud account.
+    - pwspy >=0.2.4 # Core pws package, available on backmanlab anaconda cloud account.
     - mpl_qt_viz >=1.0.7  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
-
+    - descartes
+    - cachetools >=4
 app:
   entry: PWSAnalysis
   icon: cellLogo64.png  #The logo doesn't work :(

setup.py

@@ -46,8 +46,10 @@
                         'google-auth-httplib2',
                         'google-auth-oauthlib',
                         'PyQt5',
-                        'pwspy>=0.2.3',  # Core pws package, available on backmanlab anaconda cloud account.
-                        'mpl_qt_viz>=1.0.7'],  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
+                        'pwspy>=0.2.4',  # Core pws package, available on backmanlab anaconda cloud account.
+                        'mpl_qt_viz>=1.0.7',  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
+                        'descartes',
+                        'cachetools>=4'],
       package_dir={'': 'src'},
       package_data={'pwspy_gui': ['_resources/*',
                               'PWSAnalysisApp/_resources/*']},

src/pwspy_gui/ExtraReflectanceCreator/ERWorkFlow.py

@@ -138,7 +138,7 @@ def plot(self, numericalAperture: float, saveToPdf: bool = False, saveDir: str =
 
         print("Select an ROI")
         verts = cubes['cube'].sample(n=1).iloc[0].selectLassoROI()  # Select an ROI to analyze
-        mask = Roi.fromVerts('doesntmatter', 1, verts, cubes['cube'].sample(n=1).iloc[0].data.shape[:-1])
+        mask = Roi.fromVerts(verts, cubes['cube'].sample(n=1).iloc[0].data.shape[:-1])
         self.figs.extend(er.plotExtraReflection(cubes, theoryR, matCombos, numericalAperture, mask, plotReflectionImages=True))  # TODO rather than opening a million new figures open a single window that lets you flip through them.
         if saveToPdf:
             with PdfPages(os.path.join(saveDir, f"fig_{datetime.strftime(datetime.now(), '%d-%m-%Y %HH%MM%SS')}.pdf")) as pp:
@@ -199,8 +199,7 @@ def compareDates(self):
         anis = []
         figs = []  # These lists just maintain references to matplotlib figures to keep them responsive.
         verts = self.cubes['cube'].sample(n=1).iloc[0].selectLassoROI()  # Select a random of the selected cubes and use it to prompt the user for an analysis ROI
-        mask = Roi.fromVerts('doesntmatter', 1, verts=verts,
-                             dataShape=self.cubes['cube'].sample(n=1).iloc[0].data.shape[:-1])
+        mask = Roi.fromVerts(verts=verts, dataShape=self.cubes['cube'].sample(n=1).iloc[0].data.shape[:-1])
         for mat in set(self.cubes['material']):
             c = self.cubes[self.cubes['material'] == mat]
             fig, ax = plt.subplots()

src/pwspy_gui/ExtraReflectanceCreator/examples/generateExtraReflectance.py

@@ -80,7 +80,7 @@ def processIm(im):
         matCombos = er.generateMaterialCombos(list(zip(*materials))[1])
         if plotResults:
             verts = random.choice(df['cube']).selectLassoROI()
-            roi = Roi.fromVerts('plottingArea', 1, verts, df['cube'][0].data.shape[:2])
+            roi = Roi.fromVerts(verts, df['cube'][0].data.shape[:2])
             er.plotExtraReflection(df, theoryR, matCombos, na, roi, plotReflectionImages=False)
             with PdfPages(os.path.join(rootDir, "figs.pdf")) as pp:
                 for i in plt.get_fignums():

src/pwspy_gui/PWSAnalysisApp/App.py

@@ -29,6 +29,7 @@
 from PyQt5.QtGui import QPixmap
 from PyQt5.QtWidgets import QApplication, QMessageBox, QSplashScreen
 from pwspy_gui import __version__ as version
+from pwspy_gui.PWSAnalysisApp._roiManager import _DefaultROIManager, ROIManager
 from pwspy_gui.PWSAnalysisApp.utilities import BlinderDialog, RoiConverter
 from .dialogs import AnalysisSummaryDisplay
 from ._taskManagers.analysisManager import AnalysisManager
@@ -41,21 +42,24 @@
 import pwspy.dataTypes as pwsdt
 
 
-class PWSApp(QApplication):  # TODO add a scriptable interface to load files, open roi window, run analysis etc.
+class PWSApp(QApplication):
     def __init__(self, args):
         logger = logging.getLogger(__name__)
         logger.debug("About to call PWSApp superclass constructor")
         super().__init__(args)
         logger.debug("PWSApp superclass constructor is finished")
+
+        self.roiManager: ROIManager = _DefaultROIManager()
+
         self.setApplicationName(f"PWS Analysis v{version.split('-')[0]}")
         splash = QSplashScreen(QPixmap(os.path.join(resources, 'pwsLogo.png')))
         splash.show()
         logger.debug("Initialize ERManager")
         self.ERManager = ERManager(applicationVars.extraReflectionDirectory)
         logger.debug("Finish constructing ERManager")
-        self.window = PWSWindow(self.ERManager)
-        logger.debug("Finish constructing window")
+        self.window = PWSWindow(self.ERManager, self.roiManager)
         splash.finish(self.window)
+        logger.debug("Finish constructing window")
         self.anMan = AnalysisManager(self)
         self.window.runAction.connect(self.anMan.runList)
         availableRamGigs = psutil.virtual_memory().available / 1024**3
@@ -72,6 +76,12 @@ def __init__(self, args):
         self.window.roiConvertAction.triggered.connect(self.convertRois)
         self.workingDirectory = None
 
+        # import qdarkstyle  # This looks bad
+        # dark_stylesheet = qdarkstyle.load_stylesheet_pyqt5()
+        # self.setStyleSheet(dark_stylesheet)
+
+        self.window.show()
+
     ### API
     def changeDirectory(self, directory: str, recursive: bool):
         from glob import glob
@@ -129,3 +139,9 @@ def plotSelectedCells(self, analysisName: str = None):
             analysisName = ''
         self.window.plots.setAnalysisName(analysisName)
         self.window.plots.refreshPlots()
+
+    def __del__(self):
+        try:
+            self.roiManager.close()
+        except AttributeError:  # If an error occured in the constructor the attribute may have never been created.
+            pass

src/pwspy_gui/PWSAnalysisApp/__main__.py

@@ -85,28 +85,25 @@ def exception_hook(exctype, value, traceBack):
     fHandler = logging.FileHandler(os.path.join(applicationVars.dataDirectory, f'log{datetime.now().strftime("%d%m%Y%H%M%S")}.txt'))
     fHandler.setFormatter(logging.Formatter('%(levelname)s: %(asctime)s %(name)s.%(funcName)s(%(lineno)d) - %(message)s', datefmt='%Y-%m-%d %H:%M:%S'))
     logger.addHandler(fHandler)
+    logger.setLevel(logging.INFO)
     if debugMode:
-        logger.setLevel(logging.DEBUG)
+        logging.getLogger("pwspy_gui").setLevel(logging.DEBUG)
+        logging.getLogger("pwspy").setLevel(logging.DEBUG)
         logger.info("Logger set to debug mode.")
-    else:
-        logger.setLevel(logging.INFO)
-
+
     try:
         os.environ["QT_AUTO_SCREEN_SCALE_FACTOR"] = "1"  # TODO replace these options with proper high dpi handling. no pixel specific widths.
         QApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling)
         logger.debug("About to construct `PWSApp`")
         app = PWSApp(sys.argv)
         logger.debug("Finished constructing `PWSApp`")
+
         #Testing script
         # app.changeDirectory(r'\\backmanlabnas.myqnapcloud.com\home\Year3\zstack_focusSensitivity\again', False)
-        # app.setSelectedCells([app.getLoadedCells()[0]])
+        # app.setSelectedCells(app.getLoadedCells()[:3])
         # app.plotSelectedCells()
         # app.window.plots._startRoiDrawing()
 
-        # import qdarkstyle
-        # dark_stylesheet = qdarkstyle.load_stylesheet_pyqt5()
-        # app.setStyleSheet(dark_stylesheet)
-
         if not isIpython():  # IPython runs its own QApplication so we handle things slightly different.
             sys.exit(app.exec_())
     except Exception as e:  # Save error to text file.

src/pwspy_gui/PWSAnalysisApp/_dockWidgets/AnalysisSettingsDock/widgets/SettingsFrames/_PWSSettingsFrame.py

@@ -30,7 +30,7 @@
 
 from PyQt5 import QtCore, QtGui
 from PyQt5.QtWidgets import QScrollArea, QGridLayout, QLineEdit, QLabel, QGroupBox, QHBoxLayout, QWidget, QRadioButton, \
-    QFrame, QCheckBox
+    QFrame, QCheckBox, QDoubleSpinBox
 
 from pwspy.analysis.pws import PWSAnalysisSettings
 from pwspy_gui.PWSAnalysisApp import applicationVars
@@ -112,20 +112,29 @@ def __init__(self, erManager: ERManager, cellSelector: CellSelector):
         layout = QGridLayout()
         layout.setContentsMargins(5, 1, 5, 5)
         _ = layout.addWidget
+
         orderLabel = QLabel("Filter Order")
         self.filterOrder = QHSpinBox()
         self.filterOrder.setRange(0, 6)
-        self.filterOrder.setToolTip("A lowpass filter is applied to the spectral signal to reduce noise. This determines the `order` of the digital filter.")
+        self.filterOrder.setToolTip("A low-pass filter is applied to the spectral signal to reduce noise. This determines the `order` of the digital filter.")
         orderLabel.setToolTip(self.filterOrder.toolTip())
         cutoffLabel = QLabel("Cutoff Freq.")
-        self.filterCutoff = QHDoubleSpinBox()
+        self.filterCutoff: QDoubleSpinBox = QHDoubleSpinBox()
         self.filterCutoff.setToolTip("The frequency in units of 1/wavelength for the filter cutoff.")
+        self.filterCutoff.setDecimals(3)  # Greater precision than default
         cutoffLabel.setToolTip(self.filterCutoff.toolTip())
-        _(orderLabel, 0, 0, 1, 1)
-        _(self.filterOrder, 0, 1, 1, 1)
-        _(cutoffLabel, 1, 0, 1, 1)
-        _(self.filterCutoff, 1, 1, 1, 1)
-        _(QLabel("nm<sup>-1</sup>"), 1, 2, 1, 1)
+        self.filterCheckbox = QCheckBox("Low-pass Filtering", self)
+        def stateChange(state: bool):
+            self.filterOrder.setEnabled(state)
+            self.filterCutoff.setEnabled(state)
+        self.filterCheckbox.stateChanged.connect(stateChange)
+        self.filterCheckbox.setChecked(True)  # This is just to initialize the proper state
+        _(self.filterCheckbox, 0, 0, 1, 2)
+        _(orderLabel, 1, 0, 1, 1)
+        _(self.filterOrder, 1, 1, 1, 1)
+        _(cutoffLabel, 2, 0, 1, 1)
+        _(self.filterCutoff, 2, 1, 1, 1)
+        _(QLabel("nm<sup>-1</sup>"), 2, 2, 1, 1)
         self.signalPrep.setLayout(layout)
         self._layout.addWidget(self.signalPrep, row, 0, 1, 2)
 
@@ -142,10 +151,17 @@ def __init__(self, erManager: ERManager, cellSelector: CellSelector):
         self.wavelengthStop.setToolTip("Sometimes the beginning and end of the spectrum can have very high noise. For this reason we crop the data before analysis.")
         self.wavelengthStart.setRange(300, 800)
         self.wavelengthStop.setRange(300, 800)
-        _(QLabel("Start"), 0, 0)
-        _(QLabel("Stop"), 0, 1)
-        _(self.wavelengthStart, 1, 0)
-        _(self.wavelengthStop, 1, 1)
+        self.croppingCheckbox = QCheckBox("Enable Cropping", self)
+        def cropStateChanged(state: bool):
+            self.wavelengthStop.setEnabled(state)
+            self.wavelengthStart.setEnabled(state)
+        self.croppingCheckbox.stateChanged.connect(cropStateChanged)
+        self.croppingCheckbox.setChecked(True)  # This is just to initialze the propert state.
+        _(self.croppingCheckbox, 0, 0, 1, 2)
+        _(QLabel("Start"), 1, 0)
+        _(QLabel("Stop"), 1, 1)
+        _(self.wavelengthStart, 2, 0)
+        _(self.wavelengthStop, 2, 1)
         self.cropping.setLayout(layout)
         self._layout.addWidget(self.cropping, row, 2, 1, 2)
         row += 1
@@ -200,12 +216,20 @@ def _updateSize(self):
         self._frame.setFixedHeight(height)
 
     def loadFromSettings(self, settings: PWSAnalysisSettings):
+        if settings.filterCutoff is None:
+            self.filterCheckbox.setChecked(False)
+        else:
+            self.filterCheckbox.setChecked(True)
+            self.filterCutoff.setValue(settings.filterCutoff)
         self.filterOrder.setValue(settings.filterOrder)
-        self.filterCutoff.setValue(settings.filterCutoff)
         self.polynomialOrder.setValue(settings.polynomialOrder)
         self.extraReflection.loadFromSettings(settings.numericalAperture, settings.referenceMaterial, settings.extraReflectanceId)
-        self.wavelengthStop.setValue(settings.wavelengthStop)
-        self.wavelengthStart.setValue(settings.wavelengthStart)
+        if settings.wavelengthStop is None:
+            self.croppingCheckbox.setChecked(False)
+        else:
+            self.croppingCheckbox.setChecked(True)
+            self.wavelengthStop.setValue(settings.wavelengthStop)
+            self.wavelengthStart.setValue(settings.wavelengthStart)
         self.advanced.setCheckState(2 if settings.skipAdvanced else 0)
         self.autoCorrStopIndex.setValue(settings.autoCorrStopIndex)
         self.minSubCheckBox.setCheckState(2 if settings.autoCorrMinSub else 0)
@@ -229,12 +253,15 @@ def getSettings(self) -> PWSRuntimeAnalysisSettings:
             raise ValueError("The selected reference acquisition has no valid PWS data.")
         if len(cellMeta) == 0:
             raise ValueError("No valid PWS acquisitions were selected.")
+        cutoff = self.filterCutoff.value() if self.filterCheckbox.checkState() else None
+        wvStart = self.wavelengthStart.value() if self.croppingCheckbox.checkState() else None
+        wvStop = self.wavelengthStop.value() if self.croppingCheckbox.checkState() else None
         return PWSRuntimeAnalysisSettings(settings=PWSAnalysisSettings(filterOrder=self.filterOrder.value(),
-                                                                       filterCutoff=self.filterCutoff.value(),
+                                                                       filterCutoff=cutoff,
                                                                        polynomialOrder=self.polynomialOrder.value(),
                                                                        referenceMaterial=refMaterial,
-                                                                       wavelengthStart=self.wavelengthStart.value(),
-                                                                       wavelengthStop=self.wavelengthStop.value(),
+                                                                       wavelengthStart=wvStart,
+                                                                       wavelengthStop=wvStop,
                                                                        skipAdvanced=self.advanced.checkState() != 0,
                                                                        autoCorrMinSub=self.minSubCheckBox.checkState() != 0,
                                                                        autoCorrStopIndex=self.autoCorrStopIndex.value(),