Merge pull request #60 from nel-lab/get-large-input-movie

caiman extension to get input movie using pims or caiman.load_memmap

mesmerize_core/caiman_extensions/common.py

@@ -7,6 +7,7 @@
 
 import numpy as np
 import pandas as pd
+import pims
 
 from ..batch_utils import (
  COMPUTE_BACKENDS,
@@ -17,10 +18,11 @@
  PathsSeriesExtension,
  HAS_PYQT,
 )
-from ..utils import validate_path, IS_WINDOWS, make_runfile
+from ..utils import validate_path, IS_WINDOWS, make_runfile, warning_experimental
 
 if HAS_PYQT:
  from PyQt5 import QtCore
+from caiman import load_memmap
 
 
 def validate(algo: str = None):
@@ -254,7 +256,6 @@ def run(
 
  return self.process
 
- @validate()
  def get_input_movie_path(self) -> Path:
  """
  Returns
@@ -265,6 +266,17 @@ def get_input_movie_path(self) -> Path:
 
  return self._series.paths.resolve(self._series["input_movie_path"])
 
+ @warning_experimental()
+ def get_input_movie(self) -> Union[np.ndarray, pims.FramesSequence]:
+ extension = self.get_input_movie_path().suffixes[-1]
+
+ if extension in ['.tiff', '.tif', '.btf']:
+ return pims.open(str(self.get_input_movie_path()))
+
+ elif extension in ['.mmap', '.memmap']:
+ Yr, dims, T = load_memmap(str(self.get_input_movie_path()))
+ return np.reshape(Yr.T, [T] + list(dims), order="F")
+
  @validate()
  def get_correlation_image(self) -> np.ndarray:
  """

requirements.txt

@@ -10,3 +10,5 @@ matplotlib
 click
 psutil
 PyQt5
+pims
+