From b719257daaea2deac0b9ce5ea0b7e4ad56974ae0 Mon Sep 17 00:00:00 2001
From: kushalkolar <kushalkolar@gmail.com>
Date: Fri, 24 Jun 2022 03:24:43 -0400
Subject: [PATCH 1/2] caiman extension to get input movie using pims or
 caiman.load_memmap

---
 mesmerize_core/caiman_extensions/common.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/mesmerize_core/caiman_extensions/common.py b/mesmerize_core/caiman_extensions/common.py
index 6f0ffb0..7f6e67c 100644
--- a/mesmerize_core/caiman_extensions/common.py
+++ b/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:
         """

From 149856681f42c05c10668dcfce7ad53b77825be3 Mon Sep 17 00:00:00 2001
From: kushal <kushalkolar@gmail.com>
Date: Mon, 27 Jun 2022 02:20:50 -0400
Subject: [PATCH 2/2] add pimps to requirements.txt

---
 requirements.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/requirements.txt b/requirements.txt
index 416949a..b944286 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,3 +10,5 @@ matplotlib
 click
 psutil
 PyQt5
+pims
+