Added image_utils.save_image (#45)

* added image_utils * use tmi main branch
angelolab · Nov 4, 2022 · 5645497 · 5645497
1 parent d497999
commit 5645497
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/mibi_bin_tools/bin_files.py b/mibi_bin_tools/bin_files.py
@@ -8,6 +8,7 @@
 import xarray as xr
 
 from mibi_bin_tools import io_utils, type_utils, _extract_bin
+from tmi.image_utils import save_image
 
 
 def _mass2tof(masses_arr: np.ndarray, mass_offset: float, mass_gain: float,
@@ -100,12 +101,8 @@ def _write_out(img_data: np.ndarray, out_dir: str, fov_name: str, targets: List[
             # save all first images regardless of replacing
             # if not replace (i=1), only save intensity images for specified targets
             if i == 0 or (target in list(intensities)):
-                io.imsave(
-                    os.path.join(out_dir_i, f'{target}{suffix}.tiff'),
-                    img_data[i, :, :, j].astype(save_dtype),
-                    plugin='tifffile',
-                    check_contrast=False
-                )
+                fname = os.path.join(out_dir_i, f"{target}{suffix}.tiff")
+                save_image(fname=fname, data=img_data[i, :, :, j].astype(save_dtype))
 
 
 def _find_bin_files(data_dir: str,

diff --git a/requirements.txt b/requirements.txt
@@ -3,4 +3,5 @@ matplotlib==3.4.3
 numpy>=1.21.6,<2
 pandas>=1.3.5,<2
 scikit-image>=0.19.3,<0.20
+tmi @ git+https://github.com/angelolab/tmi.git
 xarray>=2022.6.0,<2023