Move PWSExperimentPath and PWSImagePath in __init__ to be individuall…

…y defined in each example for better usability.

examples/ROItoReference.py

@@ -27,7 +27,10 @@
 import pwspy.dataTypes as pwsdt
 import matplotlib.pyplot as plt
 import numpy as np
-from examples import PWSImagePath
+
+### User Variables ###
+PWSImagePath = ...  # Set this to the path of a "Cell{X}" folder of a PWS acquisition.
+######################
 
 plt.ion()
 a = pwsdt.Acquisition(PWSImagePath).pws.toDataClass()  # Load a measurement from file.

examples/__init__.py

@@ -33,10 +33,5 @@
     opdExampleScript
     positionTransformation
 """
-import pathlib as pl
 
-# Set this to a folder containing multiple "Cell{x}" acquisition folders. Some examples will use this.
-PWSExperimentPath = pl.Path(__file__).parent.parent / 'tests' / 'resources' / 'test_data' / 'sequencer'
 
-# Set this to the "Cell{X}" folder of a PWS acquisition. Most of the examples will then refer to this file.
-PWSImagePath = PWSExperimentPath / 'Cell1'

examples/compileResults.py

@@ -21,9 +21,13 @@
 """
 import pandas
 from pwspy.analysis.compilation import PWSRoiCompiler, PWSCompilerSettings
-from examples import PWSExperimentPath
 import pwspy.dataTypes as pwsdt
 
+### User Variables ###
+PWSExperimentPath = ...  # Set this to a folder containing multiple "Cell{x}" acquisition folders. If you have downloaded the test dataset you can use `pl.Path(__file__).parent.parent / 'tests' / 'resources' / 'test_data' / 'sequencer'`
+######################
+
+
 tmpList = []
 compiler = PWSRoiCompiler(PWSCompilerSettings(reflectance=True, rms=True))
 

examples/limitedOPDSigma.py

@@ -23,7 +23,7 @@
 The phantom has a strong thin-film spectrum. This script is meant to filter out the thin film components
 of the fourier transfrom and extract RMS from what is left.
 """
-from pwspy.dataTypes import CameraCorrection, Acquisition, Roi, PwsCube, KCube
+from pwspy.dataTypes import CameraCorrection, Acquisition, PwsCube, KCube
 import matplotlib.pyplot as plt
 import scipy.signal as sps
 import os
@@ -36,7 +36,7 @@
 maskSuffix = 'resin'
 
 # identify the depth in um to which the OPD spectra need to be integrated
-integrationDepth = 2.0  ##  in um
+integrationDepth = 2.0  # in um
 isHannWindow = True  # Should Hann windowing be applied to eliminate edge artifacts?
 subtractResinOpd = True
 resetResinMasks = False

examples/opdExampleScript.py

@@ -23,10 +23,13 @@
 """
 
 import pwspy.dataTypes as pwsdt
-from mpl_qt_viz.visualizers import PlotNd
-from examples import PWSImagePath
+from mpl_qt_viz.visualizers import PlotNd  # The mpl_qt_viz library is not a dependency of PWSpy and will need to be installed separately. It can be found on Conda-Forge (conda install -c conda-forge mpl_qt_viz) or on PyPi (pip install mpl_qt_viz)
 import matplotlib.pyplot as plt
 
+### User Variables ###
+PWSImagePath = ...  # Set this to the path of a "Cell{X}" folder of a PWS acquisition.
+######################
+
 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()
 

examples/positionTransformation.py

@@ -26,39 +26,37 @@
 @author: Nick Anthony
 """
 
-if __name__ == '__main__':
-
-    import pathlib as pl
-    import matplotlib.pyplot as plt
-    from skimage.transform import AffineTransform
-    import numpy as np
-
-    plt.ion()
-    NCPath = pl.Path(r'Z:\Nick\NU-NC_EtOH fixation comparison\NC\Buccal cell')
-    NUPath = pl.Path(r'Z:\Nick\NU-NC_EtOH fixation comparison\NU\Buccal')
-
-    # Load the position list of the coverslip corners taken at the beginning of the experiment.
-    preTreatRefPositions = PositionList.fromNanoMatFile(NCPath / 'corners_list2.mat', 'TIXYDrive')
-    # Load the position list of the coverslip corners after placing the dish back on the microscope after treatment.
-    postTreatRefPositions = PositionList.fromPropertyMap(PropertyMap.loadFromFile(NUPath / 'corners.pos'))
-    # Generate an affine transform describing the difference between the two position lists.
-    transformMatrix = preTreatRefPositions.getAffineTransform(postTreatRefPositions)
-    # Load the positions of the cells we are measuring before the dish was removed.
-    preTreatCellPositions = PositionList.fromNanoMatFile(NCPath / 'cell_list.mat', 'TIXYDrive')
-    # Transform the cell positions to the new expected locations.
-    postTreatCellPositions = preTreatCellPositions.applyAffineTransform(transformMatrix)
-    # Save the new positions to a file that can be loaded by Micro-Manager.
-    postTreatCellPositions.toPropertyMap().saveToFile(NUPath / 'transformedPositions.pos')
-
-    # Plot the reference and cell positions before treatment
-    fig, ax = plt.subplots()
-    preTreatRefPositions.plot(fig, ax)
-    preTreatCellPositions.plot(fig, ax)
-
-    # Plot the reference and cell positions after treatment
-    fig2, ax2 = plt.subplots()
-    postTreatRefPositions.plot(fig2, ax2)
-    postTreatCellPositions.plot(fig2, ax2)
-
-    af = AffineTransform(np.vstack([transformMatrix, [0, 0, 1]]))
-    print(f"Scale: {af.scale}, Shear: {af.shear}, Rotation: {af.rotation / (2*np.pi) * 360}, Translation: {af.translation}")
+import pathlib as pl
+import matplotlib.pyplot as plt
+from skimage.transform import AffineTransform
+import numpy as np
+
+plt.ion()
+NCPath = pl.Path(r'Z:\Nick\NU-NC_EtOH fixation comparison\NC\Buccal cell')
+NUPath = pl.Path(r'Z:\Nick\NU-NC_EtOH fixation comparison\NU\Buccal')
+
+# Load the position list of the coverslip corners taken at the beginning of the experiment.
+preTreatRefPositions = PositionList.fromNanoMatFile(NCPath / 'corners_list2.mat', 'TIXYDrive')
+# Load the position list of the coverslip corners after placing the dish back on the microscope after treatment.
+postTreatRefPositions = PositionList.fromPropertyMap(PropertyMap.loadFromFile(NUPath / 'corners.pos'))
+# Generate an affine transform describing the difference between the two position lists.
+transformMatrix = preTreatRefPositions.getAffineTransform(postTreatRefPositions)
+# Load the positions of the cells we are measuring before the dish was removed.
+preTreatCellPositions = PositionList.fromNanoMatFile(NCPath / 'cell_list.mat', 'TIXYDrive')
+# Transform the cell positions to the new expected locations.
+postTreatCellPositions = preTreatCellPositions.applyAffineTransform(transformMatrix)
+# Save the new positions to a file that can be loaded by Micro-Manager.
+postTreatCellPositions.toPropertyMap().saveToFile(NUPath / 'transformedPositions.pos')
+
+# Plot the reference and cell positions before treatment
+fig, ax = plt.subplots()
+preTreatRefPositions.plot(fig, ax)
+preTreatCellPositions.plot(fig, ax)
+
+# Plot the reference and cell positions after treatment
+fig2, ax2 = plt.subplots()
+postTreatRefPositions.plot(fig2, ax2)
+postTreatCellPositions.plot(fig2, ax2)
+
+af = AffineTransform(np.vstack([transformMatrix, [0, 0, 1]]))
+print(f"Scale: {af.scale}, Shear: {af.shear}, Rotation: {af.rotation / (2*np.pi) * 360}, Translation: {af.translation}")

examples/roiUsageExample.py

@@ -24,11 +24,15 @@
 import matplotlib.pyplot as plt
 import pathlib
 import numpy as np
-from examples import PWSExperimentPath
-plt.ion()
 
-workingDirectory = PWSExperimentPath  # The folder that all your acquisitions are saved under.
+
+### User Variables ###
+PWSExperimentPath = ...  # Set this to a folder containing multiple "Cell{x}" acquisition folders. If you have downloaded the test dataset you can use `pl.Path(__file__).parent.parent / 'tests' / 'resources' / 'test_data' / 'sequencer'`
 analysisName = 'script'  # This will often be "p0"
+######################
+
+plt.ion()
+
 
 def plotHist(roi, rms):
     """
@@ -44,7 +48,7 @@ def plotHist(roi, rms):
     plt.hist(vals)  # Plot a histogram
 
 
-cellFolderIterator = pathlib.Path(workingDirectory).glob("Cell[0-9]")  # An iterator for all folders that are below workingDirectory and match the "regex" pattern "Cell[0-9]"
+cellFolderIterator = pathlib.Path(PWSExperimentPath).glob("Cell[0-9]")  # An iterator for all folders that are below workingDirectory and match the "regex" pattern "Cell[0-9]"
 for folder in cellFolderIterator:
     acq = pwsdt.Acquisition(folder)  # An object handling the contents of a single "Cell{X}" folder
 

examples/runPWSAnalysis.py

@@ -22,7 +22,10 @@
 
 from pwspy import analysis
 from pwspy import dataTypes as pwsdt
-from examples import PWSExperimentPath
+
+### User Variables ###
+PWSExperimentPath = ...  # Set this to a folder containing multiple "Cell{x}" acquisition folders. If you have downloaded the test dataset you can use `pl.Path(__file__).parent.parent / 'tests' / 'resources' / 'test_data' / 'sequencer'`
+######################
 
 settings = analysis.pws.PWSAnalysisSettings.loadDefaultSettings("Recommended")
 

examples/syntheticReference.py

@@ -27,7 +27,10 @@
 
 import matplotlib.pyplot as plt
 import pwspy.dataTypes as pwsdt
-from examples import PWSImagePath
+
+### User Variables ###
+PWSImagePath = ...  # Set this to the path of a "Cell{X}" folder of a PWS acquisition.
+######################
 
 plt.ion()