Merge pull request #9 from UCSB-VRL/chad/nph_with_mask_editing

Updated NPH Preduction Module for Mask Editing Feature
UCSB-VRL · Apr 25, 2023 · 5d8a720 · 5d8a720
2 parents aa19cf0 + 0afbb62
commit 5d8a720
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Showing 10 changed files with 508 additions and 200 deletions.
diff --git a/.gitignore b/.gitignore
@@ -137,3 +137,4 @@ QRBSA/src/DREAM3D-6.5.141-Linux-x86_64/*
 SpeciesTrackerAndCounter/src/runs/train/*
 *.hdf5
 
+*.tar
diff --git a/nphprediction/PythonScriptWrapper.py b/nphprediction/PythonScriptWrapper.py
@@ -40,6 +40,7 @@ def preprocess(self, bq, **kw):
         """
         Pre-process the images
         """
+        log.info('CKPT01')
         log.info('Pre-Process Options: %s' % (self.options))
         """
 	1. Get the resource image
@@ -53,7 +54,11 @@ def preprocess(self, bq, **kw):
         predictor_url = bq.service_url('image_service', path=predictor_uniq)
         log.info("predictor_URL: %s" % (predictor_url))
         predictor_path = os.path.join(kw.get('stagingPath', 'source/Scans'), self.getstrtime()+'-'+image.name + '.nii')
-
+
+        os.mkdir('source/Scans')
+        log.info('CKPT03 ' + str(os.listdir('.')))
+        log.info('CKPT04 ' + str(os.listdir('source')))
+        log.info('CKPT02 ' + str(predictor_path))
         predictor_path = bq.fetchblob(predictor_url, path=predictor_path)
         log.info("predictor_path: %s" % (predictor_path))
         #predictor_path = fetchImage(bq, predictor_url, dest=predictor_path, uselocalpath=True)
@@ -171,7 +176,7 @@ def run(self):
             print(os.listdir(results_outdir))
             self.outfiles = []
             for files in os.listdir(results_outdir):
-                if files.endswith("1.nii.gz"):
+                if files.endswith('ome.tiff'):
                     self.outfiles.append(results_outdir+files)
             bq.update_mex('Uploading Mask result')
             self.resimage = self.uploadimgservice(bq, self.outfiles)

diff --git a/nphprediction/help.html b/nphprediction/help.html
@@ -0,0 +1,31 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+
+<h2>
+    <title>Volumetric Segmentation of Brain CT Scans</title>
+</h2>
+
+<body>
+
+    <h3>About:</h3>
+    <a href="public/workflow.png" target="_blank"> <img src="public/workflow.png" /></a>
+    <p>
+		This module is for segmenting a CT scan of a brain into 3 parts: lateral ventricles, cerebral matter, and subarachnoid space using a  3D UNet. A Support Vector Machine is then used to determine if the subject has possible Normal Pressure Hydrocephalus (NPH).
+    </p>
+
+    <p>
+        <a href="https://arxiv.org/abs/1901.09088" target="_blank">Paper: Automated Segmentation of CT Scans for Normal Pressure Hydrocephalus</a>.
+    </p>
+
+    <h3>Input</h3>
+    <p> The input should be a single image or a folder of images in nifti format (ending in .nii.gz).</p>
+    <h3>Outputs</h3>
+    <ul>
+        <li><b>Info:</b> CSV file of volumetric measurements and NPH prediction.</li>
+        <li><b>Segmentation Mask:</b>A segmentation mask in nifti format. If folder of images is used, a folder of segmentation masks are returned.</li>
+      </ul>
+
+
+</body>
+
+</html>
diff --git a/nphprediction/nphprediction.xml b/nphprediction/nphprediction.xml
diff --git a/nphprediction/runtime-module.cfg b/nphprediction/runtime-module.cfg
@@ -9,7 +9,7 @@ module_enabled = True
 runtime.platforms=command
 
 [command]
-docker.image = nph-v1
+docker.image = nph-v3-mask-editor:v0.0.1
 environments = Staged,Docker
 executable = python PythonScriptWrapper.py
 files = pydist, PythonScriptWrapper.py
Original file line number	Diff line number	Diff line change
Expand Up		@@ -137,3 +137,4 @@ QRBSA/src/DREAM3D-6.5.141-Linux-x86_64/*
		SpeciesTrackerAndCounter/src/runs/train/*
		*.hdf5

		*.tar