Merge pull request #57 from Leengit/visualize_oct

BUG: Remove extraneous code and widgets from VPAWVisualizeOCT

Modules/Scripted/VPAWModel/VPAWModel.py

@@ -76,7 +76,7 @@ def registerSampleData():
     Add data sets to Sample Data module.
     """
     # It is always recommended to provide sample data for users to make it easy to try
-    # the module, but if no sample data is available then this method (and associated
+    # the module, but if no sample data are available then this method (and associated
     # startupCompeted signal connection) can be removed.
 
     pass
@@ -261,13 +261,13 @@ def updateButtonStatesAndTooltips(self):
         else:
             self.ui.linkPediatricAirwayAtlasButton.toolTip = (
                 "Install is disabled; first select a valid source code directory for"
-                + " the Pediatric Airway Atlas"
+                " the Pediatric Airway Atlas"
             )
             self.ui.linkPediatricAirwayAtlasButton.enabled = False
 
         self.ui.VPAWRootDirectory.toolTip = (
             "Directory containing FilteredControlBlindingLogUniqueScanFiltered.xls,"
-            + " images/*, and landmarks/*."
+            " images/*, and landmarks/*."
         )
         self.ui.VPAWModelDirectory.toolTip = (
             "Directory containing file named like '116(158.10-38.AM.24.Mar).pth'"
@@ -283,7 +283,7 @@ def updateButtonStatesAndTooltips(self):
         else:
             self.ui.runPediatricAirwayAtlasButton.toolTip = (
                 "Run is disabled; first select input/output root directory and models"
-                + " directory"
+                " directory"
             )
             self.ui.runPediatricAirwayAtlasButton.enabled = False
 
@@ -469,7 +469,7 @@ def linkPediatricAirwayAtlas(self, pediatricAirwayAtlasDirectory):
         stopTime = time.time()
         logging.info(
             f"Pediatric Airway Atlas installation completed in {stopTime-startTime:.2f}"
-            + " seconds",
+            " seconds",
         )
         return response
 
@@ -500,7 +500,7 @@ def ensureModulePath(self, directory):
         except ImportError:
             slicer.util.errorDisplay(
                 f"Unable to find pediatric_airway_atlas.{import_name}\n"
-                + "Check the console for details.",
+                "Check the console for details.",
                 "Install Error",
             )
             return False
@@ -615,16 +615,14 @@ def runPediatricAirwayAtlas(
         # self.convertCTScansToNRRD(vPAWRootDirectory)
         response = self.convertFCSVLandmarksToP3(
             vPAWRootDirectory, patientPrefix,
-        ) and self.runSegmentation(
-            vPAWRootDirectory, vPAWModelDirectory, patientPrefix,
-        )
+        ) and self.runSegmentation(vPAWRootDirectory, vPAWModelDirectory, patientPrefix)
         if response:
             slicer.util.infoDisplay("The pipeline has completed", "Pipeline ran")
 
         stopTime = time.time()
         logging.info(
             f"Pediatric Airway Atlas pipeline completed in {stopTime-startTime:.2f}"
-            + " seconds",
+            " seconds",
         )
         return response
 
@@ -655,11 +653,11 @@ def convertFCSVLandmarksToP3(self, vPAWRootDirectory, patientPrefix):
                 except Exception:
                     slicer.util.errorDisplay(
                         "The run failed.  It may be that a non-blank patient prefix is"
-                        + " not supported by this version of pediatric_airway_atlas"
-                        + ".conversion_utils.generate_pixel_space_landmarks."
-                        + "  Please update pediatric_airway_atlas and try again."
-                        + "  Alternatively, it may be that you entered a patient prefix"
-                        + " that does not exist.",
+                        " not supported by this version of pediatric_airway_atlas"
+                        ".conversion_utils.generate_pixel_space_landmarks."
+                        "  Please update pediatric_airway_atlas and try again."
+                        "  Alternatively, it may be that you entered a patient prefix"
+                        " that does not exist.",
                         "Run Error",
                     )
                     return False
@@ -780,11 +778,11 @@ def runSegmentation(self, vPAWRootDirectory, vPAWModelDirectory, patientPrefix):
                 except Exception:
                     slicer.util.errorDisplay(
                         "The run failed.  It may be that a non-blank patient prefix is"
-                        + " not supported by this version of pediatric_airway_atlas"
-                        + ".atlas_builder_configurable."
-                        + "  Please update pediatric_airway_atlas and try again."
-                        + "  Alternatively, it may be that you entered a patient prefix"
-                        + " that does not exist.",
+                        " not supported by this version of pediatric_airway_atlas"
+                        ".atlas_builder_configurable."
+                        "  Please update pediatric_airway_atlas and try again."
+                        "  Alternatively, it may be that you entered a patient prefix"
+                        " that does not exist.",
                         "Run Error",
                     )
                     return False

Modules/Scripted/VPAWModelOCT/VPAWModelOCT.py

@@ -73,7 +73,7 @@ def registerSampleData():
     Add data sets to Sample Data module.
     """
     # It is always recommended to provide sample data for users to make it easy to try
-    # the module, but if no sample data is available then this method (and associated
+    # the module, but if no sample data are available then this method (and associated
     # startupCompeted signal connection) can be removed.
 
     pass
@@ -240,7 +240,7 @@ def updateButtonStatesAndTooltips(self):
         else:
             self.ui.linkOCTSegButton.toolTip = (
                 "Install is disabled; first select a valid source code directory for"
-                + " the OCT Segmentation"
+                " the OCT Segmentation"
             )
             self.ui.linkOCTSegButton.enabled = False
 
@@ -435,7 +435,7 @@ def linkOCTSeg(self, octSegDirectory):
         stopTime = time.time()
         logging.info(
             f"OCT Segmentation installation completed in {stopTime-startTime:.2f}"
-            + " seconds",
+            " seconds",
         )
         return response
 
@@ -558,11 +558,7 @@ def installAndImportDependencies(self):
         self.showInstalledModules(installed_modules)
         return True
 
-    def runOCTSeg(
-        self,
-        octSegDirectory,
-        vPAWOCTConfigFile,
-    ):
+    def runOCTSeg(self, octSegDirectory, vPAWOCTConfigFile):
         """
         Run the OCT Segmentation pipeline.
         Can be used without GUI widget.
@@ -597,8 +593,7 @@ def runOCTSeg(
 
         stopTime = time.time()
         logging.info(
-            f"OCT Segmentation pipeline completed in {stopTime-startTime:.2f}"
-            + " seconds",
+            f"OCT Segmentation pipeline completed in {stopTime-startTime:.2f} seconds",
         )
         return response
 

Modules/Scripted/VPAWVisualize/VPAWVisualize.py

@@ -3,59 +3,102 @@
 import pickle as pk
 from pathlib import Path
 
-import numpy as np
-import vtk
-
 import ctk
+import numpy as np
 import qt
 import slicer
 import slicer.ScriptedLoadableModule
 import slicer.util
+import vtk
 from vpawvisualizelib.isosurfaces import isosurfaces_from_volume
 
 
-def summary_repr(contents):
+def summary_repr(contents, collapseSequences=False):
     """
     Like Python `repr`, returns a string representing the contents.  However, numpy
     arrays are summarized as their shape and unknown types are summarized by their type.
 
     Parameters
     ----------
-    contents : Python object
+    contents :
+        Python object
+    collapseSequences :
+        Set to True to summarize only the first of any list, tuple, or set that has
+        length longer than one.  In contrast, a dict will be presented in full.
 
     Returns
     -------
     A string representation of a summary of the object
+
     """
+    if isinstance(
+        contents, (bool, int, float, str, np.int32, np.int64, np.float32, np.float64),
+    ):
+        return repr(contents)
+    if isinstance(contents, (list, tuple, dict, set)) and len(contents) == 0:
+        return repr(type(contents)())
     if isinstance(contents, list):
-        return "[" + ", ".join([summary_repr(elem) for elem in contents]) + "]"
-    elif isinstance(contents, tuple):
-        if len(contents) == 1:
-            return "(" + summary_repr(contents[0]) + ",)"
-        else:
-            return "(" + ", ".join([summary_repr(elem) for elem in contents]) + ")"
-    elif isinstance(contents, dict):
+        if collapseSequences and len(contents) > 1:
+            return (
+                "["
+                + summary_repr(contents[0], collapseSequences)
+                + f", 'and {len(contents) - 1} more'"
+                + "]"
+            )
+        return (
+            "["
+            + ", ".join([summary_repr(elem, collapseSequences) for elem in contents])
+            + "]"
+        )
+    if isinstance(contents, tuple):
+        if collapseSequences and len(contents) > 1:
+            return (
+                "("
+                + summary_repr(contents[0], collapseSequences)
+                + f", 'and {len(contents) - 1} more'"
+                + ",)"
+            )
+        return (
+            "("
+            + ", ".join([summary_repr(elem, collapseSequences) for elem in contents])
+            + ",)"
+        )
+    if isinstance(contents, dict):
         return (
             "{"
             + ", ".join(
                 [
-                    summary_repr(key) + ": " + summary_repr(value)
-                    for (key, value) in contents.items()
+                    summary_repr(key, collapseSequences)
+                    + ": "
+                    + summary_repr(value, collapseSequences)
+                    for key, value in contents.items()
                 ],
             )
             + "}"
         )
-    elif isinstance(contents, set):
-        if len(contents) == 0:
-            return repr(set())
-        else:
-            return "{" + ", ".join([summary_repr(elem) for elem in contents]) + "}"
-    elif isinstance(contents, (int, float, np.float32, np.float64, bool, str)):
-        return repr(contents)
-    elif isinstance(contents, np.ndarray):
-        return repr(type(contents)) + ".shape=" + summary_repr(contents.shape)
-    else:
-        return repr(type(contents))
+    if isinstance(contents, set):
+        if collapseSequences and len(contents) > 1:
+            return (
+                "{"
+                + summary_repr(next(iter(contents)), collapseSequences)
+                + f", 'and {len(contents) - 1} more'"
+                + "}"
+            )
+        return (
+            "{"
+            + ", ".join([summary_repr(elem, collapseSequences) for elem in contents])
+            + "}"
+        )
+    if isinstance(contents, np.ndarray):
+        return (
+            repr(type(contents))
+            + "(shape="
+            + repr(contents.shape)
+            + ", dtype=np."
+            + repr(contents.dtype)
+            + ")"
+        )
+    return repr(type(contents))
 
 
 #
@@ -108,7 +151,7 @@ def registerSampleData():
     Add data sets to Sample Data module.
     """
     # It is always recommended to provide sample data for users to make it easy to try
-    # the module, but if no sample data is available then this method (and associated
+    # the module, but if no sample data are available then this method (and associated
     # startupCompeted signal connection) can be removed.
 
     pass
@@ -636,7 +679,7 @@ def loadFromP3File(self, filename, properties):
             return self.loadCenterlineFromP3FileContents(contents)
 
         print(f"File type for {filename} is not currently supported")
-        print(f"{filename} contains {summary_repr(contents)}")
+        print(f"{filename} contains {summary_repr(contents,True)}")
 
         return None
 

Modules/Scripted/VPAWVisualize/vpawvisualizelib/isosurfaces.py

@@ -1,6 +1,5 @@
-import vtk
-
 import slicer
+import vtk
 
 
 def isosurfaces_from_volume(