Eduardo Gonzalez Solares · d19b748c
--- a/stpt_pipeline/stpt_displacement.py 0 → 100644
+++ b/stpt_pipeline/stpt_displacement.py 0 → 100644
+    # read mosaic file, get delta in microns
+    mosaic_file=get_mosaic_file(this_dir)
+    dx,dy,lx,ly=read_mosaicifile_stpt(this_dir+mosaic_file)
+    delta_x,delta_y=find_delta(dx,dy)
+    # dx0,dy0 are just the coordinates of each image
+    # in columns/rows
+    dx0=np.round((dx-dx.min())/delta_x).astype(int)
+    dy0=np.round((dy-dy.min())/delta_y).astype(int)
+    # get image names and select the first optical slice
+    imgs,img_num,channel,optical_slice=get_img_list(this_dir,mosaic_size=len(dx))
+    optical_slice=optical_slice-optical_slice.min()+1
+    # read image cube
+    img_cube=get_img_cube(\
+            this_dir,imgs,img_num,channel,optical_slice,channel_to_use=channel_to_use,\
+            slice_to_use=optical_slice.min()\
+        )