Susanne Schmid
commited on
Commit
•
c71fa8b
1
Parent(s):
43339b0
Removed Info pop ups and updated description
Browse files
app.py
CHANGED
@@ -112,7 +112,7 @@ def Norm_image(vol_path,normalization_technique):
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img_load = LoadImage(pathName)
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imglist.append(img_load.flatten())
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-
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if 'MinMax' in normalization_technique:
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imgNlist.append(NormalizeMinMax(img_load).flatten())
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@@ -126,12 +126,13 @@ def Norm_image(vol_path,normalization_technique):
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if 'Percentile (10th - 90th)' in normalization_technique:
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imgNPlist.append(NormalizePercentile(img_load, 10, 90).flatten())
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gr.Info('The different normalization techniques are calculted.')
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plt.figure(11)
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imglist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=
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ax.legend()
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plt.savefig("Original.png")
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plots=["Original.png"]
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@@ -139,7 +140,7 @@ def Norm_image(vol_path,normalization_technique):
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if 'MinMax' in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=
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ax.legend()
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plt.savefig("MinMax.png")
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plots.append("MinMax.png")
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@@ -147,7 +148,7 @@ def Norm_image(vol_path,normalization_technique):
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if 'Z-Score' in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNZlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=
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ax.legend()
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plt.savefig("Zscore.png")
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plots.append("Zscore.png")
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@@ -156,7 +157,7 @@ def Norm_image(vol_path,normalization_technique):
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if 'Percentile (2th - 98th)'in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNPer98list[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=
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ax.legend()
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plt.savefig("Per98.png")
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plots.append("Per98.png")
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@@ -164,17 +165,19 @@ def Norm_image(vol_path,normalization_technique):
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if 'Percentile (10th - 90th)' in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNPlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=
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ax.legend()
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plt.savefig("Per90.png")
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plots.append("Per90.png")
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return plots
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description = 'You can upload mutiple image volumes (recommonded 3-5)
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inputs = [gr.File(file_count="multiple", label=None),gr.CheckboxGroup(["MinMax", "Z-Score", "Percentile (2th - 98th)", "Percentile (10th - 90th)"])]
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demo = gr.Interface(fn=Norm_image,
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img_load = LoadImage(pathName)
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imglist.append(img_load.flatten())
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+
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if 'MinMax' in normalization_technique:
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imgNlist.append(NormalizeMinMax(img_load).flatten())
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if 'Percentile (10th - 90th)' in normalization_technique:
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imgNPlist.append(NormalizePercentile(img_load, 10, 90).flatten())
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gr.Info('The volumes are loaded succesfully and different normalization techniques are calculted.')
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log_scale = False
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plt.figure(11)
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imglist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=log_scale,element="step", fill=False,bins=500,legend=True).set(title='Original')
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ax.legend()
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plt.savefig("Original.png")
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plots=["Original.png"]
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if 'MinMax' in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=log_scale,element="step", fill=False,bins=500,legend=True).set(title='Min-Max')
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ax.legend()
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plt.savefig("MinMax.png")
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plots.append("MinMax.png")
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if 'Z-Score' in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNZlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=log_scale,element="step", fill=False,bins=500,legend=True).set(title='Z-Score')
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ax.legend()
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plt.savefig("Zscore.png")
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plots.append("Zscore.png")
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if 'Percentile (2th - 98th)'in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNPer98list[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=log_scale,element="step", fill=False,bins=500,legend=True).set(title='Percentile 2-98')
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ax.legend()
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plt.savefig("Per98.png")
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plots.append("Per98.png")
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if 'Percentile (10th - 90th)' in normalization_technique:
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fig, ax = plt.subplots(1,1)
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for i, file in enumerate(vol_path):
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sns.histplot(data=imgNPlist[i].flatten(), kde=False, label=os.path.basename(file.name)[0:25], log_scale=log_scale,element="step", fill=False,bins=500,legend=True).set(title='Percentile 10 - 90')
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ax.legend()
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plt.savefig("Per90.png")
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plots.append("Per90.png")
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return plots
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description = 'You can upload mutiple image volumes (recommonded 3-5). The files get read by ITK so mulitple different file formats are possible (e.g. *.nii , *.nii.gz, png,..). You need to wait until the data is uploaded. \
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Once pressing submit the histograms for multiple normalization techniques are calculated. Depending on file size and selected techniques it might take a while to do the calculations. \
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\n The uploaded data is not stored and is deleted once the window is closed. '
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inputs = [gr.File(file_count="multiple", label=None),gr.CheckboxGroup(["MinMax", "Z-Score", "Percentile (2th - 98th)", "Percentile (10th - 90th)"])]
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demo = gr.Interface(fn=Norm_image,
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