moved preview QC files to qc subfolder

HMS-IDAC · Jun 25, 2021 · 86fa659 · 86fa659
1 parent f9f7d12
commit 86fa659
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Showing 3 changed files with 9 additions and 15 deletions.
diff --git a/UnMicst.py b/UnMicst.py
@@ -629,6 +629,7 @@ def singleImageInference(image, mode, pmIndex):
 
 	if not os.path.exists(args.outputPath):
 		os.makedirs(args.outputPath)
+		os.makedirs(args.outputPath + '//qc')
 
 	append_kwargs = {
 		'bigtiff': True,
@@ -651,8 +652,8 @@ def singleImageInference(image, mode, pmIndex):
 				skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Probabilities_' + str(dapiChannel) + '.tif',np.uint8(255 * PM),**append_kwargs)
 			if slice==1:
 				save_kwargs['append'] = False
-				skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',	np.uint8(255 * PM), **save_kwargs)
-				skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif', np.uint8(255 * rawI), **append_kwargs)
+				skimage.io.imsave(args.outputPath + '//qc//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',	np.uint8(255 * PM), **save_kwargs)
+				skimage.io.imsave(args.outputPath + '//qc//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif', np.uint8(255 * rawI), **append_kwargs)
 			slice = slice + 1
 
 	else:
@@ -668,12 +669,3 @@ def singleImageInference(image, mode, pmIndex):
 		skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_NucleiPM_' + str(dapiChannel) + '.tif',np.uint8(255 * nuclei), **save_kwargs)
 		del nuclei
 	UNet2D.singleImageInferenceCleanup()
-
-#aligned output files to reflect ilastik
-#outputting all classes as single file
-#handles multiple formats including tif, ome.tif, nd2, czi
-#selectable models (human nuclei, mouse nuclei, cytoplasm)
-
-#added legacy function to save output files
-#append save function to reduce memory footprint
-#added --classOrder parameter to specify which class is background, contours, and nuclei respectively
diff --git a/UnMicst1-5.py b/UnMicst1-5.py
@@ -808,6 +808,7 @@ def singleImageInference(image, mode, pmIndex):
 
 	if not os.path.exists(args.outputPath):
 		os.makedirs(args.outputPath)
+		os.makedirs(args.outputPath + '//qc')
 
 	append_kwargs = {
 		'bigtiff': True,
@@ -835,9 +836,9 @@ def singleImageInference(image, mode, pmIndex):
 					np.uint8(255 * PM), **append_kwargs)
 			if slice == 1:
 				save_kwargs['append'] = False
-				skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',
+				skimage.io.imsave(args.outputPath +  '//qc//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',
 								  np.uint8(255 * PM), **save_kwargs)
-				skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',
+				skimage.io.imsave(args.outputPath +  '//qc//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',
 								  np.uint8(255 * rawI), **append_kwargs)
 			slice = slice + 1
 

diff --git a/UnMicst2.py b/UnMicst2.py
@@ -788,6 +788,7 @@ def singleImageInference(image, mode, pmIndex):
 
     if not os.path.exists(args.outputPath):
         os.makedirs(args.outputPath)
+        os.makedirs(args.outputPath + '//qc')
 
     append_kwargs = {
         'bigtiff': True,
@@ -810,8 +811,8 @@ def singleImageInference(image, mode, pmIndex):
                 skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Probabilities_' + str(dapiChannel) + '.tif',np.uint8(255 * PM),**append_kwargs)
             if slice==1:
                 save_kwargs['append'] = False
-                skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',	np.uint8(255 * PM), **save_kwargs)
-                skimage.io.imsave(args.outputPath + '//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif', np.uint8(255 * rawI), **append_kwargs)
+                skimage.io.imsave(args.outputPath +  '//qc//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif',	np.uint8(255 * PM), **save_kwargs)
+                skimage.io.imsave(args.outputPath +  '//qc//' + fileNamePrefix[0] + '_Preview_' + str(dapiChannel) + '.tif', np.uint8(255 * rawI), **append_kwargs)
             slice = slice + 1
 
     else: