Merge branch 'main' into concat_cli

mantis/analysis/deskew.py

@@ -1,5 +1,7 @@
 import numpy as np
-import scipy
+import torch
+
+from monai.transforms.spatial.array import Affine
 
 
 def _average_n_slices(data, average_window_width=1):
@@ -116,8 +118,7 @@ def deskew_data(
     px_to_scan_ratio: float,
     keep_overhang: bool,
     average_n_slices: int = 1,
-    order: int = 1,
-    cval: float = None,
+    device='cpu',
 ):
     """Deskews fluorescence data from the mantis microscope
     Parameters
@@ -127,65 +128,60 @@ def deskew_data(
         - axis 0 corresponds to the scanning axis
         - axis 1 corresponds to the "tilted" axis
         - axis 2 corresponds to the axis in the plane of the coverslip
+    ls_angle_deg : float
+        angle of light sheet with respect to the optical axis in degrees
     px_to_scan_ratio : float
         (pixel spacing / scan spacing) in object space
         e.g. if camera pixels = 6.5 um and mag = 1.4*40, then the pixel spacing
         is 6.5/(1.4*40) = 0.116 um. If the scan spacing is 0.3 um, then
         px_to_scan_ratio = 0.116 / 0.3 = 0.386
-    ls_angle_deg : float
-        angle of light sheet with respect to the optical axis in degrees
     keep_overhang : bool
         If true, compute the whole volume within the tilted parallelepiped.
         If false, only compute the deskewed volume within a cuboid region.
     average_n_slices : int, optional
         after deskewing, averages every n slices (default = 1 applies no averaging)
-    order : int, optional
-        interpolation order (default 1 is linear interpolation)
-    cval : float, optional
-        fill value area outside of the measured volume (default None fills
-        with the minimum value of the input array)
+    device : str, optional
+        torch device to use for computation. Default is 'cpu'.
     Returns
     -------
     deskewed_data : NDArray with ndim == 3
         axis 0 is the Z axis, normal to the coverslip
         axis 1 is the Y axis, input axis 2 in the plane of the coverslip
         axis 2 is the X axis, the scanning axis
     """
-    if cval is None:
-        cval = np.min(np.ravel(raw_data))
-
     # Prepare transforms
-    Z, Y, X = raw_data.shape
-
     ct = np.cos(ls_angle_deg * np.pi / 180)
-    Z_shift = 0
-    if not keep_overhang:
-        Z_shift = int(np.floor(Y * ct * px_to_scan_ratio))
-
     matrix = np.array(
         [
             [
                 -px_to_scan_ratio * ct,
                 0,
                 px_to_scan_ratio,
-                Z_shift,
+                0,
             ],
-            [-1, 0, 0, Y - 1],
-            [0, -1, 0, X - 1],
+            [-1, 0, 0, 0],
+            [0, -1, 0, 0],
+            [0, 0, 0, 1],
         ]
     )
     output_shape, _ = get_deskewed_data_shape(
         raw_data.shape, ls_angle_deg, px_to_scan_ratio, keep_overhang
     )
 
-    # Apply transforms
-    deskewed_data = scipy.ndimage.affine_transform(
-        raw_data,
-        matrix,
-        output_shape=output_shape,
-        order=order,
-        cval=cval,
-    )
+    # convert to tensor on GPU
+    # convert raw_data to int32 if it is uint16
+    raw_data_tensor = torch.from_numpy(raw_data.astype(np.float32)).to(device)
+
+    # Returns callable
+    affine_func = Affine(affine=matrix, padding_mode="zeros", image_only=True)
+
+    # affine_func accepts CZYX array, so for ZYX input we need [None] and for ZYX output we need [0]
+    deskewed_data = affine_func(
+        raw_data_tensor[None], mode="bilinear", spatial_size=output_shape
+    )[0]
+
+    # to numpy array on CPU
+    deskewed_data = deskewed_data.cpu().numpy()
 
     # Apply averaging
     averaged_deskewed_data = _average_n_slices(

mantis/cli/deskew.py

@@ -1,9 +1,8 @@
-import multiprocessing as mp
-
 from pathlib import Path
 from typing import List
 
 import click
+import torch
 
 from iohub.ngff import open_ome_zarr
 
@@ -13,6 +12,10 @@
 from mantis.cli.parsing import config_filepath, input_position_dirpaths, output_dirpath
 from mantis.cli.utils import yaml_to_model
 
+# Needed for multiprocessing with GPUs
+# https://github.com/pytorch/pytorch/issues/40403#issuecomment-1422625325
+torch.multiprocessing.set_start_method('spawn', force=True)
+
 
 @click.command()
 @input_position_dirpaths()
@@ -21,7 +24,7 @@
 @click.option(
     "--num-processes",
     "-j",
-    default=mp.cpu_count(),
+    default=1,
     help="Number of cores",
     required=False,
     type=int,
@@ -88,3 +91,7 @@ def deskew(
             num_processes=num_processes,
             **deskew_args,
         )
+
+
+if __name__ == "__main__":
+    deskew()

mantis/cli/estimate_stabilization.py

@@ -163,7 +163,11 @@ def estimate_xy_stabilization(
     if (output_folder_path / "positions_focus.csv").exists():
         df = pd.read_csv(output_folder_path / "positions_focus.csv")
         pos_idx = str(Path(*input_data_path.parts[-3:]))
-        z_idx = list(df[df["position"] == pos_idx]["focus_idx"].replace(0, np.nan).ffill())
+        focus_idx = df[df["position"] == pos_idx]["focus_idx"]
+        # forward fill 0 values, when replace remaining NaN with the mean
+        focus_idx = focus_idx.replace(0, np.nan).ffill()
+        focus_idx = focus_idx.fillna(focus_idx.mean())
+        z_idx = focus_idx.astype(int).to_list()
     else:
         z_idx = [
             focus_from_transverse_band(

pyproject.toml

@@ -21,15 +21,16 @@ classifiers = [
 # list package dependencies here
 dependencies = [
   "copylot @ git+https://github.com/czbiohub-sf/coPylot",
-  "iohub==0.1.0.dev5",
+  "iohub==0.1.0",
   "matplotlib",
   "napari; 'arm64' in platform_machine",                 # without Qt5 and skimage
   "napari[all]; 'arm64' not in platform_machine",        # with Qt5 and skimage
   "PyQt6; 'arm64' in platform_machine",
   "natsort",
   "ndtiff>=2.0",
   "nidaqmx",
-  "numpy",
+  "numpy<2",
+  "monai",
   "pandas~=2.1",
   "pycromanager==0.28.1",
   "pydantic",