updating examples.

.gitignore

@@ -11,3 +11,4 @@ buildScripts/pyInstaller/dist/
 .idea/
 src/pwspy/_version
 *.orig
+tests/resources/test_data/

src/pwspy/dataTypes/_data.py

@@ -76,6 +76,7 @@ def index(self) -> t_.Tuple[float, ...]:
         """
         return self._index
 
+
     def plotMean(self) -> t_.Tuple[plt.Figure, plt.Axes]:
         """
 
@@ -107,7 +108,7 @@ def getMeanSpectra(self, mask: t_.Optional[t_.Union[_other.Roi, np.ndarray]] = N
         std = self.data[mask].std(axis=0)
         return mean, std
 
-    def selectLassoROI(self, displayIndex: t_.Optional[int] = None, clim: t_.Sequence = None) -> np.ndarray:
+    def selectLassoROI(self, displayIndex: t_.Optional[int] = None, clim: t_.Sequence = None) -> _other.Roi:
         """
         Allow the user to draw a `freehand` ROI on an image of the acquisition.
 
@@ -134,7 +135,7 @@ def onSelect(verts):
         fig.show()
         while plt.fignum_exists(fig.number):
             fig.canvas.flush_events()
-        return np.array(Verts[0])
+        return _other.Roi.fromVerts(np.array(Verts[0]), self.data.shape[:2])
 
     def selectRectangleROI(self, displayIndex: t_.Optional[int] = None) -> np.ndarray:
         """

src/pwspy/examples/ROItoMirror.py

@@ -17,24 +17,27 @@
 
 # -*- coding: utf-8 -*-
 """
-This script Allows the user to select a region of an PwsCube. the spectra of this
+This script allows the user to select a region of an PwsCube. the spectra of this
 region is then averaged over the X and Y dimensions. This spectra is then saved
 as a reference dataTypes with the same initial dimensions.
 Can help to make a reference when you don't actually have one for some reason
 """
 
-from pwspy.dataTypes import PwsCube
+import pwspy.dataTypes as pwsdt
 import matplotlib.pyplot as plt
 import numpy as np
 from pwspy.examples import PWSImagePath
 
 if __name__ == '__main__':
-    a = PwsCube.loadAny(PWSImagePath)
+    plt.ion()
+    a = pwsdt.Acquisition(PWSImagePath).pws.toDataClass()
 
-    mask = a.selectLassoROI()
-    spec, std = a.getMeanSpectra(mask)
+    roi = a.selectLassoROI()
+    spec, std = a.getMeanSpectra(mask=roi)
     newData = np.zeros(a.data.shape)
     newData[:, :, :] = spec[np.newaxis, np.newaxis, :]
-    ref = PwsCube(newData, a.metadata)
+    ref = pwsdt.PwsCube(newData, a.metadata)
 
     plt.plot(a.wavelengths, spec)
+
+    a = 1

src/pwspy/examples/__init__.py

@@ -33,4 +33,8 @@
     opdExampleScript
 """
 
+# Set this to a folder containing multiple "Cell{x}" acquisition folders. Some examples will use this.
+PWSExperimentPath = r"C:\Users\backman05\Documents\Bitbucket\pwspython\tests\resources\seqTest"
+
+# Set this to the "Cell{X}" folder of a PWS acquisition. Most of the examples will then refer to this file.
 PWSImagePath = r'\\backmanlabnas.myqnapcloud.com\home\Year2\canvassing\Cell868'

src/pwspy/examples/limitedOPDSigma.py

@@ -78,7 +78,7 @@
                 resinRoi = resin.metadata.acquisitionDirectory.loadRoi(maskSuffix, 1)
             else:
                 print('Select a region containing only resin.')
-                resinRoi = Roi.fromVerts(resin.selectLassoROI(), resin.data.shape[:2])
+                resinRoi = resin.selectLassoROI()
                 resin.metadata.acquisitionDirectory.saveRoi(maskSuffix, 1, resinRoi)
             resin.data -= resin.data.mean(axis=2)[:, :, np.newaxis]
             opdResin, xvals = resin.getOpd(isHannWindow, indexOpdStop=None, mask=resinRoi.mask)

src/pwspy/examples/opdExampleScript.py

@@ -8,22 +8,28 @@
 
     import pwspy.dataTypes as pwsdt
     from mpl_qt_viz.visualizers import PlotNd
+    from pwspy.examples import PWSImagePath
+    import matplotlib.pyplot as plt
 
-    imageDirectory = r'\\backmanlabnas.myqnapcloud.com\home\Year3\ethanolTimeSeries\LTL20l_Pure\Track_3hrs\Cell3'
+    plt.ion()  # Without this we will get a crash when trying to open the PlotNd window because a Qt application loop must be running.
+    plt.figure()
 
-    acquisition = pwsdt.Acquisition(imageDirectory)
+    acquisition = pwsdt.Acquisition(PWSImagePath)
 
     roiSpecs = acquisition.getRois()
     print("ROIs:\n", roiSpecs)
 
-    PwsCube = acquisition.pws.toDataClass()
-    kCube = pwsdt.KCube.fromPwsCube(PwsCube)
-    del PwsCube
+    analysis = acquisition.pws.loadAnalysis(acquisition.pws.getAnalyses()[0])  # Load a reference to an analysis file.
+    kCube = analysis.reflectance  # Load the processed `reflectance` array from the analysis file.
 
-    opd, opdValues = kCube.getOpd(useHannWindow= False, indexOpdStop = 50)
+    opd, opdValues = kCube.getOpd(useHannWindow=False, indexOpdStop=50)  # Use FFT to transform the reflectance array to OPD
 
-    ri = 1.37
+    # Scale the opdValues to give estimated depth instead of raw OPD. Factor of 2 because light is making a round-trip.
+    ri = 1.37  # Estimated RI of livecell chromatin
     opdValues = opdValues / (2 * ri)
 
     plotWindow = PlotNd(opd, names=('y', 'x', 'depth'),
-                        indices=(None, None, opdValues), title="Estimated Depth")
+                        indices=(None, None, opdValues), title="Estimated Depth")
+
+    a = 1
+    a = 1

src/pwspy/examples/plotITOThinFilmCalibration.py

@@ -41,7 +41,7 @@ def proc(im: PwsCube):
     return im, ref
 
 if __name__ == '__main__':
-    subDir = r'J:\Calibrations\ITOThinFilm\LCPWS1' # Use '*' to include all subdirectories
+    subDir = r'J:\Calibrations\ITOThinFilm\LCPWS1'  # Use '*' to include all subdirectories
     dateStart = '1-16-2020'
     dateEnd = None
     templateName = '1_16_2020'