Merge pull request #9 from nanthony21/dev

0.1.11 RC

conda.recipe/meta.yaml

@@ -32,8 +32,8 @@ requirements:
     - google-auth-httplib2
     - google-auth-oauthlib
     - pyqt =5
-    - pwspy >=0.2.8 # 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
+    - pwspy >=0.2.12 # 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
 app:

setup.py

@@ -46,8 +46,8 @@
                         'google-auth-httplib2',
                         'google-auth-oauthlib',
                         'PyQt5',
-                        'pwspy>=0.2.8',  # 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
+                        'pwspy>=0.2.12',  # 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'],
       package_dir={'': 'src'},

src/pwspy_gui/ExtraReflectanceCreator/ERWorkFlow.py

@@ -14,7 +14,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with PWSpy.  If not, see <https://www.gnu.org/licenses/>.
-
+import dataclasses
 import hashlib
 import os
 from datetime import datetime
@@ -24,7 +24,7 @@
 from PyQt5.QtWidgets import QWidget
 from matplotlib import animation
 
-from pwspy.dataTypes import CameraCorrection, Acquisition, ICMetaData, PwsCube
+from pwspy.dataTypes import CameraCorrection, Acquisition, PwsMetaData, PwsCube
 from pwspy_gui.ExtraReflectanceCreator.widgets.dialog import IndexInfoForm
 from pwspy.dataTypes import Roi
 from pwspy import dateTimeFormat
@@ -39,11 +39,17 @@
 from mpl_qt_viz.visualizers import PlotNd, DockablePlotWindow
 import pathlib as pl
 
+DirectoryDataFrame = t_.NewType("DirectoryDataFrame", pd.DataFrame)  # Type alias representing the data frame returned by `scanDirectory`
+# Has columns "setting", "cube", "material"
+
 
+@dataclasses.dataclass
 class Directory:
-    def __init__(self, df: pd.DataFrame, camCorr: CameraCorrection):
-        self.dataframe = df
-        self.cameraCorrection = camCorr
+    """
+    Groups together relevant data for a given "System Directory" in the ERCreator raw data collection.
+    """
+    dataframe: DirectoryDataFrame
+    cameraCorrection: CameraCorrection
 
 
 def scanDirectory(directory: str) -> Directory:
@@ -75,28 +81,34 @@ def scanDirectory(directory: str) -> Directory:
         m = matMap[filelist[-2]]
         file = Acquisition(file).pws.filePath  # old pws is saved directly in the "Cell{X}" folder. new pws is saved in "Cell{x}/PWS" the Acquisition class helps us abstract that out and be compatible with both.
         rows.append({'setting': s, 'material': m, 'cube': file})
-    df = pd.DataFrame(rows)
-    return Directory(df, cam)
+    df: DirectoryDataFrame = pd.DataFrame(rows)
+    return Directory(dataframe=df, cameraCorrection=cam)
 
 
 class DataProvider:
-    def __init__(self, df: pd.DataFrame, camCorr: CameraCorrection):
-        self._df = df
-        self._cameraCorrection = camCorr
-        self._cubes = None
+    """
+    This object manages caching data and processing new data when it needs to be loaded.
+
+    Args:
+        directory: The Directory object providing a reference to the actual data.
+    """
+    def __init__(self, directory: Directory):
+        self._df = directory.dataframe
+        self._cameraCorrection = directory.cameraCorrection
+        self._cubes: pd.DataFrame = None
 
-    def getCubes(self):
+    def getCubes(self) -> t_.Optional[pd.DataFrame]:
         return self._cubes
 
-    def getDataFrame(self):
+    def getDataFrame(self) -> pd.DataFrame:
         return self._df
 
     def loadCubes(self, includeSettings: t_.List[str], binning: int, parallelProcessing: bool):
         df = self._df[self._df['setting'].isin(includeSettings)]
         if binning is None:
             args = {'correction': None, 'binning': None}
             for cube in df['cube']:
-                md = ICMetaData.loadAny(cube)
+                md = PwsMetaData.loadAny(cube)
                 if md.binning is None:
                     raise Exception("No binning metadata found. Please specify a binning setting.")
                 elif md.cameraCorrection is None:
@@ -182,7 +194,7 @@ def plot(self, includeSettings: t_.List[str], binning: int, parallelProcessing:
         print("Select an ROI")
         roi = cubes['cube'].sample(n=1).iloc[0].selectLassoROI()  # Select an ROI to analyze
         cubeDict = cubes.groupby('setting').apply(lambda df: df.groupby('material')['cube'].apply(list).to_dict()).to_dict()  # Transform data frame to a dict of dicts of lists for input to `plot`
-        self.figs.extend(er.plotExtraReflection(cubeDict, theoryR, matCombos, numericalAperture, roi))
+        self.figs.extend(er.plotExtraReflection(cubeDict, theoryR, matCombos, roi))
 
     def save(self, includeSettings: t_.List[str], binning: int, parallelProcessing: bool, numericalAperture: float, parentWidget: QWidget):
         self.loadIfNeeded(includeSettings, binning, parallelProcessing)
@@ -199,16 +211,19 @@ def save(self, includeSettings: t_.List[str], binning: int, parallelProcessing:
             erCube, rExtraDict = er.generateRExtraCubes(combos, theoryR, numericalAperture)
             dock = DockablePlotWindow(title=setting)
             dock.addWidget(
-                PlotNd(erCube.data, title='Mean',
+                PlotNd(erCube.data,
+                       title='Mean',
                        indices=[range(erCube.data.shape[0]), range(erCube.data.shape[1]),
-                                erCube.wavelengths]),
+                                erCube.wavelengths],
+                       names=('y', 'x', 'lambda')),
                 title='Mean'
             )
             for matCombo, rExtraArr in rExtraDict.items():
                 dock.addWidget(
                     PlotNd(rExtraArr, title=matCombo,
                            indices=[range(erCube.data.shape[0]), range(erCube.data.shape[1]),
-                                    erCube.wavelengths]),
+                                    erCube.wavelengths],
+                           names=('y', 'x', 'lambda')),
                     title=str(matCombo)
                 )
             logger = logging.getLogger(__name__)
@@ -284,5 +299,5 @@ def directoryChanged(self, directory: str) -> t_.Set[str]:
         """
         self.currDir = directory
         directory = self.fileStruct[directory]
-        self.dataprovider = DataProvider(directory.dataframe, directory.cameraCorrection)
+        self.dataprovider = DataProvider(directory)
         return set(self.dataprovider.getDataFrame()['setting'])

src/pwspy_gui/PWSAnalysisApp/_dockWidgets/AnalysisSettingsDock/runtimeSettings.py

@@ -88,8 +88,8 @@ def getExtraReflectanceMetadata(self) -> pwsdt.ERMetaData:
 class PWSRuntimeAnalysisSettings(AbstractRuntimeAnalysisSettings):  # Inherit docstring
     settings: PWSAnalysisSettings
     extraReflectanceMetadata: typing.Optional[pwsdt.ERMetaData]
-    referenceMetadata: pwsdt.ICMetaData
-    cellMetadata: typing.List[pwsdt.ICMetaData]
+    referenceMetadata: pwsdt.PwsMetaData
+    cellMetadata: typing.List[pwsdt.PwsMetaData]
     analysisName: str
 
     def getSaveableSettings(self) -> PWSAnalysisSettings:
@@ -98,10 +98,10 @@ def getSaveableSettings(self) -> PWSAnalysisSettings:
     def getAnalysisName(self) -> str:
         return self.analysisName
 
-    def getReferenceMetadata(self) -> pwsdt.ICMetaData:
+    def getReferenceMetadata(self) -> pwsdt.PwsMetaData:
         return self.referenceMetadata
 
-    def getCellMetadatas(self) -> typing.Sequence[pwsdt.ICMetaData]:
+    def getCellMetadatas(self) -> typing.Sequence[pwsdt.PwsMetaData]:
         return self.cellMetadata
 
     def getExtraReflectanceMetadata(self) -> pwsdt.ERMetaData:

src/pwspy_gui/PWSAnalysisApp/_dockWidgets/CellSelectorDock/widgets.py

@@ -26,7 +26,7 @@
     QInputDialog, QHeaderView
 
 from pwspy_gui.PWSAnalysisApp.sharedWidgets import ScrollableMessageBox
-from pwspy.dataTypes import Acquisition, ICMetaData, DynMetaData
+from pwspy.dataTypes import Acquisition, PwsMetaData, DynMetaData
 
 from pwspy_gui.PWSAnalysisApp.sharedWidgets.dictDisplayTree import DictDisplayTreeDialog
 from pwspy_gui.PWSAnalysisApp.sharedWidgets.tables import NumberTableWidgetItem
@@ -349,7 +349,7 @@ def _deleteAnalysisByName(self):
         else:
             ret = ScrollableMessageBox.question(self, "Delete Analysis?",
                 f"Are you sure you want to delete {anName} from:"
-                f"\nPWS: {', '.join([os.path.split(i.acquisitionDirectory.filePath)[-1] for i in deletableCells if isinstance(i, ICMetaData)])}"
+                f"\nPWS: {', '.join([os.path.split(i.acquisitionDirectory.filePath)[-1] for i in deletableCells if isinstance(i, PwsMetaData)])}"
                 f"\nDynamics: {', '.join([os.path.split(i.acquisitionDirectory.filePath)[-1] for i in deletableCells if isinstance(i, DynMetaData)])}")
             if ret == QMessageBox.Yes:
                 [i.removeAnalysis(anName) for i in deletableCells]
@@ -485,7 +485,7 @@ def updateReferences(self, state: bool, items: t_.List[CellTableWidgetItem]):
 
     @property
     def selectedReferenceMeta(self) -> t_.Optional[Acquisition]:
-        """Returns the ICMetadata that have been selected. Return None if nothing is selected."""
+        """Returns the PwsMetaData that have been selected. Return None if nothing is selected."""
         items: List[ReferencesTableItem] = self.selectedItems()
         assert len(items) <= 1
         if len(items) == 0:

src/pwspy_gui/PWSAnalysisApp/_dockWidgets/ResultsTableDock/__init__.py

@@ -30,7 +30,7 @@
 from ...componentInterfaces import ResultsTableController
 
 if typing.TYPE_CHECKING:
-    from pwspy.dataTypes import Acquisition, ICMetaData
+    from pwspy.dataTypes import Acquisition, PwsMetaData
     from pwspy.analysis.pws import PWSAnalysisSettings
     from pwspy.analysis.warnings import AnalysisWarning
 
@@ -135,7 +135,7 @@ def _handleCompilationResults(self, inVal: typing.List[typing.Tuple[Acquisition,
 
 
 class CompilationSummaryDisplay(QDialog):
-    def __init__(self, parent: typing.Optional[QWidget], warnings: typing.List[typing.Tuple[ICMetaData, typing.List[typing.Tuple[PWSRoiCompilationResults, typing.Optional[typing.List[AnalysisWarning]]]]]], analysisName: str = '', analysisSettings: PWSAnalysisSettings = None):
+    def __init__(self, parent: typing.Optional[QWidget], warnings: typing.List[typing.Tuple[PwsMetaData, typing.List[typing.Tuple[PWSRoiCompilationResults, typing.Optional[typing.List[AnalysisWarning]]]]]], analysisName: str = '', analysisSettings: PWSAnalysisSettings = None):
         super().__init__(parent=parent)
         self.setWindowTitle("Compilation Summary")
         layout = QVBoxLayout()
@@ -146,7 +146,7 @@ def __init__(self, parent: typing.Optional[QWidget], warnings: typing.List[typin
         self._addWarnings(warnings)
         self.show()
 
-    def _addWarnings(self, warnings: typing.List[typing.Tuple[ICMetaData, typing.List[typing.Tuple[ConglomerateCompilerResults, typing.Optional[typing.List[AnalysisWarning]]]]]]):
+    def _addWarnings(self, warnings: typing.List[typing.Tuple[PwsMetaData, typing.List[typing.Tuple[ConglomerateCompilerResults, typing.Optional[typing.List[AnalysisWarning]]]]]]):
         for meta, roiList in warnings:
             item = QTreeWidgetItem(self.warningTree)
             item.setText(0, meta.filePath)

src/pwspy_gui/PWSAnalysisApp/_dockWidgets/ResultsTableDock/widgets.py

@@ -83,6 +83,8 @@ def _plotOpd(self):
         fig, ax = plt.subplots()
         ax.plot(self.results.pws.opdIndex, self.results.pws.opd)
         fig.suptitle(f"{self.cellPathLabel.text()}/Cell{self.cellNumLabel.text()}")
+        ax.set_ylabel("Amplitude")
+        ax.set_xlabel("OPD (um)")
         fig.show()
 
 

src/pwspy_gui/PWSAnalysisApp/_roiManager.py

@@ -26,7 +26,26 @@ def updateRoi(self, roiFile: pwsdt.RoiFile, roi: pwsdt.Roi):
         self.roiUpdated.emit(roiFile)
 
     def createRoi(self, acq: pwsdt.Acquisition, roi: pwsdt.Roi, roiName: str, roiNumber: int, overwrite: bool = False) -> pwsdt.RoiFile:
-        roiFile = acq.saveRoi(roiName, roiNumber, roi, overwrite=overwrite)
+        """
+
+        Args:
+            acq: The acquisition to save the ROI to
+            roi: The ROI to save.
+            roiName: The name to save the ROI as.
+            roiNumber: The number to save the ROI as.
+            overwrite: Whether to overwrite existing ROIs with conflicting name/number combo.
+
+        Returns:
+            A reference to the created ROIFile
+
+        Raises:
+            OSError: If `overwrite` is false and an ROIFile for this name and number already exists.
+
+        """
+        try:
+            roiFile = acq.saveRoi(roiName, roiNumber, roi, overwrite=overwrite)
+        except OSError as e:
+            raise e
         self._cache[self._getCacheKey(roiFile)] = roiFile
         self.roiCreated.emit(roiFile, overwrite)
         return roiFile

src/pwspy_gui/PWSAnalysisApp/_taskManagers/analysisManager.py

@@ -34,7 +34,7 @@
 from pwspy.analysis.pws import PWSAnalysis
 from pwspy_gui.PWSAnalysisApp._dockWidgets.AnalysisSettingsDock.runtimeSettings import PWSRuntimeAnalysisSettings, DynamicsRuntimeAnalysisSettings
 from pwspy.analysis.warnings import AnalysisWarning
-from pwspy.dataTypes import ICRawBase, ICMetaData, DynMetaData
+from pwspy.dataTypes import ICRawBase, PwsMetaData, DynMetaData
 from pwspy.utility.fileIO import loadAndProcess
 if typing.TYPE_CHECKING:
     from pwspy_gui.PWSAnalysisApp.App import PWSApp
@@ -90,7 +90,7 @@ def runSingle(self, anSettings: AbstractRuntimeAnalysisSettings) -> Tuple[str, A
         if correctionsOk:
             if isinstance(anSettings, PWSRuntimeAnalysisSettings):
                 AnalysisClass = PWSAnalysis
-                refMeta: ICMetaData
+                refMeta: PwsMetaData
             elif isinstance(anSettings, DynamicsRuntimeAnalysisSettings):
                 AnalysisClass = DynamicsAnalysis
                 refMeta: DynMetaData
@@ -180,7 +180,7 @@ def __init__(self, cellMetas, analysis, anName, cameraCorrection, userSpecifiedB
         def run(self):
             try:
                 self.warnings = loadAndProcess(self.cellMetas, processorFunc=self._process, initArgs=[self.analysis, self.anName, self.cameraCorrection, self.userSpecifiedBinning],
-                                     parallel=self.parallel, initializer=self._initializer) # Returns a list of Tuples, each tuple containing a list of warnings and the ICmetadata to go with it.
+                                     parallel=self.parallel, initializer=self._initializer) # Returns a list of Tuples, each tuple containing a list of warnings and the PwsMetaData to go with it.
             except Exception as e:
                 import traceback
                 trace = traceback.format_exc()

src/pwspy_gui/PWSAnalysisApp/dialogs.py

@@ -36,7 +36,7 @@
 
 if typing.TYPE_CHECKING:
     from typing import Optional, List, Tuple
-    from pwspy.dataTypes import ICMetaData
+    from pwspy.dataTypes import PwsMetaData
     from pwspy.analysis.compilation import PWSRoiCompilationResults
     from pwspy.analysis.pws import PWSAnalysisSettings
     from pwspy.analysis.warnings import AnalysisWarning
@@ -84,7 +84,7 @@ def show(self):
 
 
 class AnalysisSummaryDisplay(QDialog):
-    def __init__(self, parent: Optional[QWidget], warnings: List[Tuple[List[AnalysisWarning], ICMetaData]], analysisName: str = '', analysisSettings: PWSAnalysisSettings = None):
+    def __init__(self, parent: Optional[QWidget], warnings: List[Tuple[List[AnalysisWarning], PwsMetaData]], analysisName: str = '', analysisSettings: PWSAnalysisSettings = None):
         super().__init__(parent=parent)
         self.analysisName = analysisName
         self.analysisSettings = analysisSettings
@@ -100,7 +100,7 @@ def __init__(self, parent: Optional[QWidget], warnings: List[Tuple[List[Analysis
         self.setWindowTitle(f"Analysis Summary: {analysisName}")
         self.show()
 
-    def _addWarnings(self, warnings: List[Tuple[List[AnalysisWarning],ICMetaData]]):
+    def _addWarnings(self, warnings: List[Tuple[List[AnalysisWarning],PwsMetaData]]):
          for cellWarns, cell in warnings:
             item = QTreeWidgetItem(self.warnList)
             item.setText(0, cell.filePath)