Merge branch 'main' into Dev_Issue_templates

Author: DKuppens

.github/pull_request_template.md

@@ -0,0 +1,13 @@
+### Describe the changes you have made in this PR
+
+_A clear and concise description of what you want to happen_
+
+### Link this PR to an issue [optional]
+
+Fixes _#ISSUE-NUMBER_
+
+### Checklist
+
+- [ ] Self-review of changed code
+- [ ] Added automated tests where applicable
+- [ ] Update Docs & Guides

.gitignore

@@ -1,6 +1,7 @@
 .idea*
 .github/*
-!.github/ISSUE_TEMPLATE/
+.github/ISSUE_TEMPLATE/
+.github/pull_request_template.md
 __pycache__/
 *.nii.gz
 bvals.txt

src/original/PvH_KB_NKI/DWI_Examples.py

@@ -14,44 +14,47 @@
 import matplotlib.pyplot as plt
 import pathlib
 
-#Load some DWI data
-file=pathlib.Path(__file__)
-file_path = file.with_name('IVIM_b0_15_150_500.npy').as_posix()
-DWI_data = np.load(file_path)
+def example():
+    #Load some DWI data
+    file=pathlib.Path(__file__)
+    file_path = file.with_name('IVIM_b0_15_150_500.npy').as_posix()
+    DWI_data = np.load(file_path)
 
-# Specify b values that are in the data
-bvalues = [0, 15, 150, 500]
+    # Specify b values that are in the data
+    bvalues = [0, 15, 150, 500]
 
-# Specifiy if you want to plot the results
-plot_results = False
+    # Specifiy if you want to plot the results
+    plot_results = False
 
-# Generate ADC map and define the min and max b value that will be used for ADC fitting
-ADClog, b0_intercept, used_bvalues = generate_ADC_standalone(DWI_data,bvalues, bmin=150, bmax=500)
+    # Generate ADC map and define the min and max b value that will be used for ADC fitting
+    ADClog, b0_intercept, used_bvalues = generate_ADC_standalone(DWI_data,bvalues, bmin=150, bmax=500)
 
-# Generate ADC and define the min and max b value that will be used for ADC fitting as well as the max b value
-# that will be used for separate Dstar fitting
-ADClog, perfFrac, Dstar = generate_IVIMmaps_standalone(DWI_data, bvalues, bminADC=150, bmaxADC=500, bmaxDstar=150)
-Slice = 5
+    # Generate ADC and define the min and max b value that will be used for ADC fitting as well as the max b value
+    # that will be used for separate Dstar fitting
+    ADClog, perfFrac, Dstar = generate_IVIMmaps_standalone(DWI_data, bvalues, bminADC=150, bmaxADC=500, bmaxDstar=150)
+    Slice = 5
 
-if plot_results == True:
-    # Plot the ADC, f and D* maps
-    fig, axes = plt.subplots(1, 3, figsize=(10, 5))
+    if plot_results == True:
+        # Plot the ADC, f and D* maps
+        fig, axes = plt.subplots(1, 3, figsize=(10, 5))
 
-    axes[0].imshow(ADClog[:,Slice,:], cmap='viridis', vmin=0, vmax=5)
-    axes[0].set_title("ADC")
-    axes[0].axis('off')
+        axes[0].imshow(ADClog[:,Slice,:], cmap='viridis', vmin=0, vmax=5)
+        axes[0].set_title("ADC")
+        axes[0].axis('off')
 
-    axes[1].imshow(perfFrac[:,Slice,:], cmap='viridis', vmin=0, vmax=1)
-    axes[1].set_title("f map")
-    axes[1].axis('off')
+        axes[1].imshow(perfFrac[:,Slice,:], cmap='viridis', vmin=0, vmax=1)
+        axes[1].set_title("f map")
+        axes[1].axis('off')
 
-    axes[2].imshow(Dstar[:,Slice,:], cmap='viridis', vmin=0, vmax=200)
-    axes[2].set_title("D*")
-    axes[2].axis('off')
+        axes[2].imshow(Dstar[:,Slice,:], cmap='viridis', vmin=0, vmax=200)
+        axes[2].set_title("D*")
+        axes[2].axis('off')
 
-    plt.tight_layout()  # Adjust spacing between subplots
-    plt.show()
+        plt.tight_layout()  # Adjust spacing between subplots
+        plt.show()
 
-print("finish")
+    print("finish")
 
 
+if __name__ == '__main__':
+    example()