From 3b504bf15b3c5ca0a1e87b18a431a66f21227200 Mon Sep 17 00:00:00 2001
From: Steve Pieper <pieper@isomics.com>
Date: Wed, 8 Nov 2023 18:50:53 -0500
Subject: [PATCH] ENH: dicom url retries and code cleanup

Catch if the returned data is not as expected and if
so do a retry.  Based on testing with a Google DICOMweb
store about 5-10 request were incomplete on a several hundred
slice dataset but no error code was reported, just truncated data.
There's no clear reason to why these failures occur, but
retrying implemented here has always resulted in good data
during testing so far.
---
 .../DICOMPlugins/DICOMScalarVolumePlugin.py   | 29 ++++++++++++-------
 1 file changed, 19 insertions(+), 10 deletions(-)

diff --git a/Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py b/Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py
index 9b363955db0..68b210b03a2 100644
--- a/Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py
+++ b/Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py
@@ -35,7 +35,7 @@ def __init__(self, epsilon=0.01):
         self.acquisitionModeling = None
         self.defaultStudyID = 'SLICER10001'  # TODO: What should be the new study ID?
         self.urlHandlerInterval = 300 # ms
-        self.urlHandlerTimeout = 120 # seconds
+        self.urlHandlerTimeout = 60 # seconds
 
         self.tags['sopClassUID'] = "0008,0016"
         self.tags['photometricInterpretation'] = "0028,0004"
@@ -409,7 +409,6 @@ def loadFilesWithSeriesReader(self, imageIOName, files, name, grayscale=True):
         logging.info("Loading with imageIOName: %s" % imageIOName)
         reader.Update()
 
-        slicer.modules.reader = reader
         if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
             errorStrings = (imageIOName, vtk.vtkErrorCode.GetStringFromErrorCode(reader.GetErrorCode()))
             logging.error("Could not read scalar volume using %s approach.  Error is: %s" % errorStrings)
@@ -431,9 +430,6 @@ def loadFilesWithSeriesReader(self, imageIOName, files, name, grayscale=True):
         volumeNode.SetRASToIJKMatrix(reader.GetRasToIjkMatrix())
         volumeNode.CreateDefaultDisplayNodes()
 
-        slicer.modules.DICOMInstance.reader = reader
-        slicer.modules.DICOMInstance.imageChangeInformation = imageChangeInformation
-
         return volumeNode
 
     def setVolumeNodeProperties(self, volumeNode, loadable):
@@ -529,8 +525,7 @@ def _processURLHandler(self, urlHandler, volumeNode, urls):
         framesByURL = urlHandler.getFrames()
         volumeArray = slicer.util.arrayFromVolume(volumeNode)
         elapsedTime = time.time() - self._urlHandlerStartTime
-        msg = _("{framesThisLoad} of {frames} in {elapsedTime:.3g}").format(framesThisLoad=len(framesByURL), frames=volumeArray.shape[0], elapsedTime=elapsedTime)
-        print(msg) # TODO
+        msg = _("{framesThisLoad} of {frames} in {elapsedTime:.3f}").format(framesThisLoad=len(framesByURL), frames=volumeArray.shape[0], elapsedTime=elapsedTime)
         logging.info(msg)
         if len(framesByURL) > 0:
             for url,frame in framesByURL.items():
@@ -539,8 +534,20 @@ def _processURLHandler(self, urlHandler, volumeNode, urls):
                 rescaleIntercept = float(rescaleInterceptValue) if rescaleInterceptValue != "" else 0.
                 rescaleSlope = float(rescaleSlopeValue) if rescaleSlopeValue != "" else 1.
                 sliceIndex = urls.index(url)
-                volumeArray[sliceIndex] = rescaleIntercept + rescaleSlope * frame
+                try:
+                    volumeArray[sliceIndex] = rescaleIntercept + rescaleSlope * frame.reshape(volumeArray[sliceIndex].shape)
+                except ValueError:
+                    logging.error(f"Incorrect frame size {frame.shape} not {volumeArray[sliceIndex].shape}")
+                    logging.error(f"retrying {url}")
+                    urlHandler.startRequest([url])
             slicer.util.arrayFromVolumeModified(volumeNode)
+            displayNode = volumeNode.GetDisplayNode()
+            if displayNode.GetNumberOfWindowLevelPresets() > 0:
+                displayNode.SetWindowLevelFromPreset(0)
+            else:
+                displayNode.AutoWindowLevelOff()
+                displayNode.AutoWindowLevelOn()
+
         if not urlHandler.requestFinished():
             if elapsedTime > self.urlHandlerTimeout:
                 logging.error("Download timeout")
@@ -550,8 +557,8 @@ def _processURLHandler(self, urlHandler, volumeNode, urls):
                 qt.QTimer.singleShot(self.urlHandlerInterval, callback)
         else:
             rate = (volumeArray.size * volumeArray.itemsize) / elapsedTime / 1024. / 1024.
-            logging.info(f"Download time {elapsedTime:.3g} at {rate:.2g} mebibytes/second") # TODO i18n
-            print(f"Download time {elapsedTime:.3g} at {rate:.2g} mebibytes/second")
+            msg = "Download time {elapsedTime:.2f} at {rate:.2f} mebibytes/second".format(elapsedTime=elapsedTime, rate=rate)
+            logging.info(msg)
 
     def load(self, loadable, readerApproach=None):
         """Load the select as a scalar volume using desired approach
@@ -564,6 +571,8 @@ def load(self, loadable, readerApproach=None):
             # - data comes from a URL, so parse metadata from dicom to slicer conventions
             # - create a placeholder volumeNode that can be populated by the downloader
             # - rely on files having already been sorted during examine step
+            if not hasattr(slicer.modules, "dicomURLHandlers"):
+                slicer.modules.dicomURLHandlers = {}
             if urlScheme in slicer.modules.dicomURLHandlers:
                 # first, initiate the request
                 urlHandler = slicer.modules.dicomURLHandlers[urlScheme]