@sjcrh/proteinpaint-server 2.61.1 → 2.62.0

package/src/serverconfig.js

@@ -55,6 +55,7 @@ if (!serverconfig.clustalo) serverconfig.clustalo = 'clustalo'
 if (!serverconfig.Rscript) serverconfig.Rscript = 'Rscript'
 if (!serverconfig.gfServer) serverconfig.gfServer = 'gfServer'
 if (!serverconfig.gfClient) serverconfig.gfClient = 'gfClient'
+// NOTE: will set other cmd paths that require binpath after it's filled-in below
 
 /******************
 	APPLY OVERRIDES 
@@ -103,6 +104,8 @@ if (!serverconfig.binpath) {
 		}
 	}
 }
+// defaults tool paths, for those that require binpath
+if (!serverconfig.plotBrainImaging) serverconfig.plotBrainImaging = `${serverconfig.binpath}/utils/plotBrainImaging.py`
 
 if (serverconfig.debugmode) {
 	// only apply optional routeSetters in debugmode

package/utils/plotBrainImaging.py

@@ -0,0 +1,73 @@
+import nibabel as nib  # Library for loading data from neuroimaging file formats such as NIfTI
+import matplotlib.pyplot as plt
+import numpy as np
+import sys
+import io
+
+if len(sys.argv) <= 1:
+	print('python3 '+sys.argv[0]+' <path/to/template/file> <path/to/label/file> indexL indexF, indexT')
+	sys.exit(1)
+
+templateFile = sys.argv[1]
+labelFile = sys.argv[2]
+
+# load data from nifti files 
+template = nib.load(templateFile).get_fdata()
+labels = nib.load(labelFile).get_fdata()
+labels = np.ma.masked_where(labels == 0, labels) # Mask labels where they are 0
+
+l = int(sys.argv[3]) if len(sys.argv) > 3 else 70
+f = int(sys.argv[4]) if len(sys.argv) > 4 else 110
+t = int(sys.argv[5]) if len(sys.argv) > 5 else 80
+
+# extract slices l (left, sagittal), f (front, coronal), t (top, axial) from the template and label data
+left_slice = template[l,:,:]
+front_slice = template[:,f,:]
+top_slice = template[:,:,t]
+
+left_label = labels[l,:,:]
+front_label = labels[:,f,:]
+top_label = labels[:,:,t]
+
+
+# adjust the orientation of the plots by flipping and rotating
+left_slice = np.rot90(left_slice)
+left_label = np.rot90(left_label)
+
+front_slice = np.flip(np.rot90(front_slice),axis=1)
+front_label = np.flip(np.rot90(front_label),axis=1)
+
+top_slice = np.flip(np.rot90(top_slice),axis=1)
+top_label = np.flip(np.rot90(top_label),axis=1)
+
+
+# create three subplots for sagittal, coronal and axial plane
+fig, ax = plt.subplots(1, 3)
+vmin = 0
+vmax = 100
+alpha = 0.5
+ax[0].imshow(left_slice, 'gray', filternorm=False, vmin=vmin, vmax=vmax)
+ax[0].imshow(left_label, 'jet', alpha=alpha, filternorm=False,vmin=0,vmax=102)
+ax[0].axis('off')
+ax[0].text(0, 0.5, 'P', fontsize=12, color='white', ha='center', va='center', transform=ax[0].transAxes)
+ax[0].text(0.5, 1, 'S', fontsize=12, color='white', ha='center', va='center', transform=ax[0].transAxes)
+
+ax[1].imshow(front_slice, 'gray', filternorm=False, vmin=vmin, vmax=vmax)
+ax[1].imshow(front_label, cmap='jet', alpha=alpha, filternorm=False,vmin=0,vmax=102)
+ax[1].axis('off')
+ax[1].text(0, 0.5, 'R', fontsize=12, color='white', ha='center', va='center', transform=ax[1].transAxes)
+ax[1].text(0.5, 1, 'S', fontsize=12, color='white', ha='center', va='center', transform=ax[1].transAxes)
+
+ax[2].imshow(top_slice, 'gray', filternorm=False, vmin=vmin, vmax=vmax)
+ax[2].imshow(top_label, cmap='jet', alpha=alpha, filternorm=False,vmin=0,vmax=102)
+ax[2].axis('off')
+ax[2].text(0, 0.5, 'R', fontsize=12, color='white', ha='center', va='center', transform=ax[2].transAxes)
+ax[2].text(0.5, 1, 'A', fontsize=12, color='white', ha='center', va='center', transform=ax[2].transAxes)
+fig.subplots_adjust(wspace=0, hspace=0)
+
+# Output the image data to stdout
+buf = io.BytesIO()
+plt.savefig(buf, format='png', bbox_inches='tight', facecolor='k')
+buf.seek(0)
+sys.stdout.buffer.write(buf.getvalue())
+plt.close()