rearrange example doc page. Minor fixes to various examples.

docs/source/examples.rst

@@ -3,23 +3,25 @@ Examples
 If you don't have PWS experimental data to run these examples with you can find a dataset that is used for automated testing
 on Zenodo here: https://zenodo.org/record/5976039#.Yf6aPt_MJPY
 
-Performing FFT on the raw data to get a view of the estimated depth of cell features
---------------------------------------------------------------------------------------
-.. literalinclude:: ../../examples/opdExampleScript.py
+Running basic PWS analysis on a single image.
+-----------------------------------------------------------------------------------------
+This example runs the PWS analysis on a single measurement. The results of the analysis will be saved alongside the raw data
+under the `analyses` folder. Running this example may be required in order for other examples which require that analysis results
+already be available.
+
+.. literalinclude:: ../../examples/runPWSAnalysis.py
    :language: python
    :linenos:
 
-.. image:: ../resources/opdExample.gif
-
-
-Brief example of basic PWS analysis to produce Sigma, Reflectance, Ld, and other images.
------------------------------------------------------------------------------------------
-.. literalinclude:: ../../examples/runPWSAnalysis.py
+Performing FFT to visualize the estimated depth of cell features
+--------------------------------------------------------------------------------------
+.. literalinclude:: ../../examples/opdExampleScript.py
    :language: python
    :linenos:
 
+.. image:: ../resources/opdExample.gif
 
-Use the `compilation` functionality to reduce analysis results to a table of values of average values within an ROI
+Compile analysis results to a table of average values within each ROI
 ----------------------------------------------------------------------------------------------------------------------
 .. literalinclude:: ../../examples/compileResults.py
    :language: python
@@ -54,4 +56,4 @@ Generating new position lists to enable colocalized measurements on multiple sys
 --------------------------------------------------------------
 .. literalinclude:: ../../examples/positionTransformation.py
    :language: python
-   :linenos:
+   :linenos:

examples/ROItoReference.py

@@ -27,9 +27,10 @@
 import pwspy.dataTypes as pwsdt
 import matplotlib.pyplot as plt
 import numpy as np
+import pathlib as pl
 
 ### User Variables ###
-PWSImagePath = ...  # Set this to the path of a "Cell{X}" folder of a PWS acquisition.
+PWSImagePath: pl.Path = ... # Set this to the path of a "Cell{X}" folder of a PWS acquisition.
 ######################
 
 plt.ion()

examples/compileResults.py

@@ -22,9 +22,10 @@
 import pandas
 from pwspy.analysis.compilation import PWSRoiCompiler, PWSCompilerSettings
 import pwspy.dataTypes as pwsdt
+import pathlib as pl
 
 ### 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'`
+PWSExperimentPath: pl.Path = ...  # 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'`
 ######################
 
 

examples/limitedOPDSigma.py

@@ -28,10 +28,11 @@
 import scipy.signal as sps
 import os
 import numpy as np
+import pathlib as pl
 
 '''User Input'''
-path = r'2_7_2019 11.07'
-refName = 'Cell999'  # This is an PwsCube of glass, used for normalization.
+path: pl.Path = ...
+refName = 'Cell3'  # This is an PwsCube of glass, used for normalization.
 cellNames = ['Cell1', 'Cell2']  # , 'Cell3', 'Cell4','Cell5']
 maskSuffix = 'resin'
 
@@ -71,7 +72,7 @@
         if resetResinMasks:
             [resin.metadata.acquisitionDirectory.deleteRoi(name, num) for name, num, fformat in resin.metadata.acquisitionDirectory.getRois() if name == maskSuffix]
         if maskSuffix in [name for name, number, fformat in resin.metadata.acquisitionDirectory.getRois()]:
-            resinRoi = resin.metadata.acquisitionDirectory.loadRoi(maskSuffix, 1)
+            resinRoi = resin.metadata.acquisitionDirectory.loadRoi(maskSuffix, 1).getRoi()
         else:
             print('Select a region containing only resin.')
             resinRoi = resin.selectLassoROI()
@@ -86,6 +87,7 @@
     ax.legend()
     plt.pause(0.2)
 
+print("Beginning processing.")
 rmses = {}  # Store the rms maps for later saving
 for cellName in cellNames:
     cube = PwsCube.fromMetadata(Acquisition(os.path.join(path, cellName)).pws)

examples/opdExampleScript.py

@@ -25,9 +25,11 @@
 import pwspy.dataTypes as pwsdt
 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
+import pathlib as pl
+from PyQt5.QtWidgets import QApplication
 
 ### User Variables ###
-PWSImagePath = ...  # Set this to the path of a "Cell{X}" folder of a PWS acquisition.
+PWSImagePath: pl.Path = ... # 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.
@@ -47,5 +49,7 @@
 ri = 1.37  # Estimated RI of livecell chromatin
 opdValues = opdValues / (2 * ri)
 
+app = QApplication([])  # Start a QApplication instance to run the PlotNd qwidget
 plotWindow = PlotNd(opd, names=('y', 'x', 'depth'),
                     indices=(None, None, opdValues), title="Estimated Depth")
+app.exec()

examples/runPWSAnalysis.py

@@ -22,9 +22,10 @@
 
 from pwspy import analysis
 from pwspy import dataTypes as pwsdt
+import pathlib as pl
 
 ### 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'`
+PWSExperimentPath: pl.Path = ...  # 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")
@@ -42,3 +43,5 @@
 acq.pws.saveAnalysis(results, 'myAnalysis', overwrite=True)  # Save our analysis results to file in the default location alongside the raw data under the `analyses` folder.
 
 loadedResults = acq.pws.loadAnalysis('myAnalysis')  # This is just going to be a copy of `results`, loaded from file.
+
+print(f"Saved anlysis `myAnalysis` to {acq.filePath}")

examples/syntheticReference.py

@@ -24,7 +24,6 @@
 """
 
 import copy
-
 import matplotlib.pyplot as plt
 import pwspy.dataTypes as pwsdt