use int16 throughout

khanlab · Sep 15, 2024 · 3dedae2 · 3dedae2
1 parent 8943f63
commit 3dedae2
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/workflow/scripts/apply_basic_flatfield_corr_zarr.py b/workflow/scripts/apply_basic_flatfield_corr_zarr.py
@@ -41,7 +41,7 @@
     #now we want to apply correction to all images
     #define a function to map
     def apply_basic_parallel(x):
-        return np.reshape(basic.transform(x.squeeze()),(1,1,img_shape[0],img_shape[1])).astype('uint16')
+        return np.reshape(basic.transform(x.squeeze()),(1,1,img_shape[0],img_shape[1])).astype('int16')
     arr_corr = da.map_blocks(apply_basic_parallel,arr_chan)
 
     chan_arr_list.append(arr_corr)

diff --git a/workflow/scripts/tif_to_zarr.py b/workflow/scripts/tif_to_zarr.py
@@ -59,7 +59,7 @@ def single_imread(*args):
 
 #rescale intensities, and recast 
 darr = darr * snakemake.params.intensity_rescaling
-darr = darr.astype('uint16')
+darr = darr.astype('int16')
 
 #now we can do the computation itself, storing to zarr
 print('writing images to zarr with dask')

diff --git a/workflow/scripts/tif_to_zarr_gcs.py b/workflow/scripts/tif_to_zarr_gcs.py
@@ -77,7 +77,7 @@ def build_zstack(gcs_uris,fs):
 
 #rescale intensities, and recast 
 darr = darr * snakemake.params.intensity_rescaling
-darr = darr.astype('uint16')
+darr = darr.astype('int16')
 
 #now we can do the computation itself, storing to zarr
 print('writing images to zarr with dask')