add example

examples/nd2_deskew.py

@@ -0,0 +1,50 @@
+# pip install pims_nd2
+from pims import ND2_Reader
+from pycudadecon.affine import affineGPU
+from skimage.io import imsave
+import numpy as np
+import os
+
+# needed to flip the sign on the transform
+DEFAULT_TMAT = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0.70711, 0, 1, 0], [0, 0, 0, 1]])
+
+
+def deskew_file(path, tmat=DEFAULT_TMAT, mip=True):
+    """Deskews an nd2 file at `path` using matrix tmat.
+
+    Will create a new folder (with the same name as the file)
+    of multichannel deskewed files for each timepoint.
+
+    Args:
+        path (str): the nd2 file to process
+        tmat (np.ndarray): the transformation matrix
+        mip (bool): Whether to write a MIP file
+    """
+    tmat = np.array(tmat)
+    dirname, fname = os.path.split(path)
+    fname, ext = os.path.splitext(fname)
+    outdir = os.path.join(dirname, fname + "_deskewed")
+    os.makedirs(outdir, exist_ok=True)
+    with ND2_Reader(path) as frames:
+        frames.bundle_axes = "czyx"
+        for frame in frames:
+            print(f"processing frame: {frame.frame_no + 1:4} of {len(frames)}")
+
+            # do the actual deskew to each channel
+            # the .T rotates it 90 degrees
+            out = np.stack([affineGPU(chan, tmat).T for chan in frame])
+            dst = os.path.join(outdir, f"{fname}_{frame.frame_no:04}.tif")
+
+            # could add metadata here for voxel sizes
+            imsave(dst, np.transpose(out, (1, 0, 2, 3)), imagej=True)
+            if mip:
+                mipdir = os.path.join(outdir, "MIPs")
+                os.makedirs(mipdir, exist_ok=True)
+                dst = os.path.join(mipdir, f"{fname}_{frame.frame_no:04}_mip.tif")
+                imsave(dst, out.max(1), imagej=True)
+
+
+if __name__ == "__main__":
+    import sys
+
+    deskew_file(sys.argv[1])