Merge pull request #11 from nanthony21/dev

Allow OPD filtering in GUI

conda.recipe/meta.yaml

@@ -16,7 +16,7 @@ build:
 
 requirements:
   build:
-    - python >=3.7
+    - python >=3.7,<3.10  # In python 3.10 a change occurred so that PyQt no longer implicitly converts float to int. causees crashes.
     - setuptools
     - setuptools_scm
 
@@ -32,7 +32,7 @@ requirements:
     - google-auth-httplib2
     - google-auth-oauthlib
     - pyqt =5
-    - pwspy >=0.2.12 # Core pws package, available on backmanlab anaconda cloud account.
+    - pwspy >=0.2.13 # Core pws package, available on backmanlab anaconda cloud account.
     - mpl_qt_viz >1.0.9  # Plotting package available on PyPi and the backmanlab anaconda cloud account and conda-forge. Written for this project by Nick Anthony
     - descartes
     - cachetools >=4

setup.py

@@ -35,7 +35,7 @@
       author='Nick Anthony',
       author_email='[email protected]',
       url='https://github.com/nanthony21/pwspy_gui',
-      python_requires='>=3.7',
+      python_requires='>=3.7,<3.10',  # In python 3.10 a chnage occured which means that PyQt no longer implicitly converts float to int. Causes crashes.
       install_requires=['numpy',
                         'matplotlib',
                         'psutil',
@@ -46,7 +46,7 @@
                         'google-auth-httplib2',
                         'google-auth-oauthlib',
                         'PyQt5',
-                        'pwspy>=0.2.12',  # Core pws package, available on backmanlab anaconda cloud account.
+                        'pwspy>=0.2.13',  # Core pws package, available on backmanlab anaconda cloud account.
                         'mpl_qt_viz>1.0.9',  # Plotting package available on PyPi and the backmanlab anaconda cloud account. Written for this project by Nick Anthony
                         'descartes',
                         'cachetools>=4'],

src/pwspy_gui/ExtraReflectanceCreator/ERWorkFlow.py

@@ -227,6 +227,8 @@ def save(self, includeSettings: t_.List[str], binning: int, parallelProcessing:
                     title=str(matCombo)
                 )
             logger = logging.getLogger(__name__)
+            erCube.data[np.isnan(erCube.data)] = 0  # Somehow a nan can still get through. This will mess everything up.
+            erCube.data[erCube.data < 0] = 0
             logger.info(f"Final data max is {erCube.data.max()}")
             logger.info(f"Final data min is {erCube.data.min()}")
             self.figs.append(dock)  # keep track of opened figures.

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

@@ -170,7 +170,8 @@ def cropStateChanged(state: bool):
         self.polySub = QGroupBox("Polynomial Subtraction")
         self.polySub.setFixedSize(150, 50)
         self.polySub.setToolTip("A polynomial is fit to each spectrum and then it is subtracted from the spectrum."
-                                        "This is so that we remove effects of absorbtion and our final signal is only due to interference")
+                                "This is so that we remove effects of absorbtion and our final signal is only due to interference"
+                                "For liquid covered samples this is always set to 0. For samples in air a 2nd order polynomial is used.")
         layout = QGridLayout()
         layout.setContentsMargins(5, 1, 5, 5)
         _ = layout.addWidget
@@ -179,8 +180,30 @@ def cropStateChanged(state: bool):
         _(self.polynomialOrder, 0, 1, 1, 1)
         self.polySub.setLayout(layout)
         self._layout.addWidget(self.polySub, row, 0, 1, 2)
+
+        # WaveNumber Filtering
+        self.waveNumberCutoff = QHDoubleSpinBox()
+        self.waveNumberCutoff.setValue(4.3)  # OPD = estimated depth * 2(roundtrip) * 1.37 (RI of cell). DOF=1.1um -> OPD = 2.95. To achieve 5% attenuation at 2.95um a 3dB cutoff of 4.3 is selected (4th-order butterworth)
+        self.cutoffWaveNumber = QCheckBox("Perform Filtering")
+        self.cutoffWaveNumber.stateChanged.connect(lambda state: self.waveNumberCutoff.setEnabled(state != QtCore.Qt.Unchecked))
+        self.cutoffWaveNumber.setCheckState(QtCore.Qt.Checked)
+        self.cutoffWaveNumber.setCheckState(QtCore.Qt.Unchecked)  # Default to off
+
+        layout = QGridLayout()
+        layout.setContentsMargins(5, 1, 5, 5)
+
+        layout.addWidget(self.cutoffWaveNumber, 0, 0, 1, 2)
+        layout.addWidget(QLabel("OPD Cutoff (um)"), 1, 0, 1, 1)
+        layout.addWidget(self.waveNumberCutoff, 1, 1, 1, 1)
+        wnFilter = QGroupBox("OPD Filtering")
+        wnFilter.setLayout(layout)
+        wnFilter.setToolTip("A 4th order buttersworth filter will be applied to the spectra (x axis: wavenumber) at the specified cutoff frequency."
+                            "The cutoff is the frequency at which the attenuation will be -3dB. After the cutoff the attenuation slope will be 80dB per decade.")
+        self._layout.addWidget(wnFilter, row, 2, 1, 2)
+
         row += 1
 
+
         '''Advanced Calculations'''
         self.advanced = CollapsibleSection('Skip Advanced Analysis', 200, self)
         self.advanced.stateChanged.connect(self._updateSize)
@@ -235,6 +258,11 @@ def loadFromSettings(self, settings: PWSAnalysisSettings):
         self.minSubCheckBox.setCheckState(2 if settings.autoCorrMinSub else 0)
         self.relativeUnits.setCheckState(2 if settings.relativeUnits else 0)
         self.hardwareCorrections.loadCameraCorrection(settings.cameraCorrection)
+        if settings.waveNumberCutoff is None:
+            self.cutoffWaveNumber.setCheckState(QtCore.Qt.Unchecked)
+        else:
+            self.cutoffWaveNumber.setCheckState(QtCore.Qt.Checked)
+            self.waveNumberCutoff.setValue(settings.waveNumberCutoff)
 
     def getSettings(self) -> PWSRuntimeAnalysisSettings:
         erMetadata, refMaterial, numericalAperture = self.extraReflection.getSettings()
@@ -268,7 +296,8 @@ def getSettings(self) -> PWSRuntimeAnalysisSettings:
                                                                        numericalAperture=numericalAperture,
                                                                        relativeUnits=self.relativeUnits.checkState() != 0,
                                                                        cameraCorrection=self.hardwareCorrections.getCameraCorrection(),
-                                                                       extraReflectanceId=erMetadata.idTag if erMetadata is not None else None),
+                                                                       extraReflectanceId=erMetadata.idTag if erMetadata is not None else None,
+                                                                       waveNumberCutoff=self.waveNumberCutoff.value() if self.cutoffWaveNumber.checkState != QtCore.Qt.Unchecked else None),
                                           extraReflectanceMetadata=erMetadata,
                                           referenceMetadata=refMeta,
                                           cellMetadata=cellMeta,

src/pwspy_gui/PWSAnalysisApp/_dockWidgets/AnalysisSettingsDock/widgets/SettingsFrames/_sharedWidgets/__init__.py

@@ -17,8 +17,7 @@
 
 from __future__ import annotations
 import os
-from typing import Optional, Tuple
-
+import typing as t_
 from PyQt5 import QtGui, QtCore
 from PyQt5.QtGui import QPalette, QValidator, QDoubleValidator
 from PyQt5.QtWidgets import QGroupBox, QWidget, QVBoxLayout, QLabel, QLineEdit, QPushButton, QHBoxLayout, QMessageBox, QGridLayout, QSpinBox, QDoubleSpinBox, \
@@ -28,8 +27,7 @@
 from pwspy_gui.PWSAnalysisApp.sharedWidgets import CollapsibleSection
 from pwspy.dataTypes import CameraCorrection, ERMetaData
 from pwspy.utility.reflection import reflectanceHelper, Material
-import typing
-if typing.TYPE_CHECKING:
+if t_.TYPE_CHECKING:
     from pwspy_gui.sharedWidgets.extraReflectionManager import ERManager
 
 
@@ -83,7 +81,7 @@ def __init__(self, parent: QWidget, erManager: ERManager):
         layout.addLayout(rLayout)
         self.setLayout(layout)
 
-    def getSettings(self) -> Tuple[ERMetaData, Material, float]:
+    def getSettings(self) -> t_.Tuple[ERMetaData, Material, float]:
         self._initializeERSelector()
         if self.ERExplorer.getSelectedMetadata() is None:
             ans = QMessageBox.question(self, "Uh", "An extra reflectance cube has not been selected. Do you want to ignore this important correction?")
@@ -98,7 +96,7 @@ def getSettings(self) -> Tuple[ERMetaData, Material, float]:
         refMaterial = Material[self.refMaterialCombo.currentText()]
         return erMd, refMaterial, numericalAperture
 
-    def getSelectedERMetadata(self) -> Optional[ERMetaData]:
+    def getSelectedERMetadata(self) -> t_.Optional[ERMetaData]:
         return self.ERExplorer.getSelectedMetadata()
 
     def loadFromSettings(self, numericalAperture: float, referenceMaterial: Material, extraReflectanceId: str):
@@ -123,7 +121,7 @@ def _initializeERSelector(self):
         if self.ERExplorer is None:  # Don't initialize the ERSelector window until we actually need it. It can be slow to initiate
             self.ERExplorer = self._erManager.createSelectorWindow(self)
 
-            def extraReflectionChanged(md: Optional[ERMetaData]):
+            def extraReflectionChanged(md: t_.Optional[ERMetaData]):
                 if md is None:
                     self.RSubtractionNameLabel.setText('None')
                 else:
@@ -177,7 +175,7 @@ def getCameraCorrection(self) -> CameraCorrection:
             cameraCorrection = None
         return cameraCorrection
 
-    def loadCameraCorrection(self, camCorr: Optional[CameraCorrection] = None):
+    def loadCameraCorrection(self, camCorr: t_.Optional[CameraCorrection] = None):
         if camCorr is None: #Automatic camera corrections
             self.setCheckState(2)
         else:
@@ -234,9 +232,9 @@ def wheelEvent(self, event):
     return HumbleDoubleSpinBox
 
 
-QHSpinBox = humble(QSpinBox)
-QHDoubleSpinBox = humble(QDoubleSpinBox)
-QHComboBox = humble(QComboBox)
+QHSpinBox: t_.Type[QSpinBox] = humble(QSpinBox)
+QHDoubleSpinBox: t_.Type[QDoubleSpinBox] = humble(QDoubleSpinBox)
+QHComboBox: t_.Type[QComboBox] = humble(QComboBox)
 
 
 class VerticallyCompressedWidget(QWidget):

src/pwspy_gui/sharedWidgets/extraReflectionManager/_ERSelectorWindow.py

@@ -76,9 +76,9 @@ def isChecked(self) -> bool:
 class ERSelectorWindow(QDialog):
     selectionChanged = QtCore.pyqtSignal(object) #Usually an ERMetaData object, sometimes None
 
-    # noinspection PyUnresolvedReferences
     def __init__(self, manager: ERManager, parent: Optional[QWidget] = None):
         self._manager = manager
+        self._plots = []  # Use this to maintain references to plots
         self._selectedMetadata: Optional[pwsdt.ERMetaData] = None
         super().__init__(parent)
         self.setModal(False)
@@ -154,7 +154,7 @@ def displayInfo(self, item: ERTreeWidgetItem):
 
     def _plot3dData(self, widgetItem):
         er = pwsdt.ExtraReflectanceCube.fromHdfFile(self._manager._directory, widgetItem.name)
-        PlotNd(er.data, indices=[range(er.data.shape[0]), range(er.data.shape[1]), er.wavelengths])
+        self._plots.append(PlotNd(er.data, indices=[range(er.data.shape[0]), range(er.data.shape[1]), er.wavelengths]))
 
     def _downloadCheckedItems(self):
         try :

src/pwspy_gui/sharedWidgets/utilityWidgets.py

@@ -33,10 +33,10 @@ def _resize(self, width, height):
         newWidth = height * self._aspect #the ideal width based on the new commanded height
         #Now determine which of the new dimensions to use.
         if width > newWidth:
-            self.setMaximumWidth(newWidth)
+            self.setMaximumWidth(int(newWidth))
             self.setMaximumHeight(QWIDGETSIZE_MAX)
         else:
-            self.setMaximumHeight(newHeight)
+            self.setMaximumHeight(int(newHeight))
             self.setMaximumWidth(QWIDGETSIZE_MAX)
 
     def setAspect(self, aspect: float):