add resizing options for pre-registration matching

HDIprep/hdi_prep.py

@@ -1121,7 +1121,7 @@ def ApplyMask(self):
             hdi_imp.hdi.data.processed_image = tmp_im
 
     # Add function for exporting UMAP nifti image
-    def ExportNifti1(self, output_dir, padding=None):
+    def ExportNifti1(self, output_dir, padding=None, target_size=None):
         """Exporting hyperspectral images resulting from UMAP and
         spatially mapping UMAP, or exporting processed histology images. Both of these
         conditions cant be true. One or the other will be exported, and it will be
@@ -1154,11 +1154,11 @@ def ExportNifti1(self, output_dir, padding=None):
                 # Otherwise export the image
                 else:
                     # Export the original image
-                    ExportNifti(hdi_imp.hdi.data.image, im_name, padding)
+                    ExportNifti(hdi_imp.hdi.data.image, im_name, padding, target_size)
             # Otherwise export the processed image
             else:
                 # Use utils export nifti function
-                ExportNifti(hdi_imp.hdi.data.processed_image, im_name, padding)
+                ExportNifti(hdi_imp.hdi.data.processed_image, im_name, padding, target_size)
             # Add exported file names to class object -- connect input file name with the exported name
             connect_dict.update({f: im_name})
 

HDIprep/utils.py

@@ -7,6 +7,7 @@
 import pandas as pd
 import nibabel as nib
 from pathlib import Path
+from skimage.transform import resize
 
 # Define function
 def CreateHyperspectralImage(embedding, array_size, coordinates, scale=True):
@@ -84,7 +85,7 @@ def CreateHyperspectralImageRectangular(embedding, array_size, coordinates, scal
     # Return the hyperspectral image
     return im
 
-def ExportNifti(image, filename, padding=None):
+def ExportNifti(image, filename, padding=None, target_size=None):
     """This function will export your final images to nifti format for image
     registration with elastix.
 
@@ -100,6 +101,9 @@ def ExportNifti(image, filename, padding=None):
 
     # Print update
     print("Exporting nifti image stack...")
+    # Check to see if resizing
+    if target_size is not None:
+        image = resize(im,target_size)
     # Check to see if padding
     if padding is not None:
         image = np.pad(