From c5ac6346bc90627b36f50acfbca0e0c5fb1bb563 Mon Sep 17 00:00:00 2001
From: Wim Pomp <w.pomp@nki.nl>
Date: Mon, 17 Oct 2022 20:16:28 +0200
Subject: [PATCH] - make it work on Linux again too

---
 README.md           | 2 +-
 issfile/__init__.py | 9 +++++----
 setup.py            | 2 +-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 17d06bf..faebfb6 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@ Metadata is also saved in the tiffs in the description tag.
 
     with IssFile(file) as iss:
         image = iss.get_image(c=1, t=5)
-        carpet = iss.get_carpet(c=1, t=5)
+        carpet, (time, x, y, z) = iss.get_carpet(c=1, t=5)
     
         plt.figure()
         plt.imshow(image)
diff --git a/issfile/__init__.py b/issfile/__init__.py
index dc34247..82d1118 100644
--- a/issfile/__init__.py
+++ b/issfile/__init__.py
@@ -17,7 +17,7 @@ class TiffFile(IJTiffFile):
         if 'processes' not in kwargs:
             kwargs['processes'] = 'all'
         super().__init__(*args, **kwargs)
-        self.iss = iss
+        self.iss = pickle.dumps(iss)  # force iss to be transferred to other processes in pickled state
         self.bar = bar
 
     def __getstate__(self):
@@ -27,6 +27,8 @@ class TiffFile(IJTiffFile):
         self.bar.update()
 
     def compress_frame(self, frame):
+        if isinstance(self.iss, bytes):
+            self.iss = pickle.loads(self.iss)
         if frame[0]:
             frame, metadata = self.iss.get_carpet(*frame[1:])
             ifd, offsets = super().compress_frame(frame.astype(self.dtype))
@@ -89,10 +91,9 @@ class IssFile:
     def get_image(self, c, t):
         assert c < self.shape[2] and t < self.shape[3], \
             f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[3]}'
-        frame = c + 2 * t * self.shape[2]
+        frame = int(c) + 2 * int(t) * self.shape[2]
         frame_bytes = self.shape[0] * self.shape[1] * self.delta
         data = []
-        # TODO: RuntimeWarning: overflow encountered in long_scalars for big files in next line
         for address in range(frame * frame_bytes, (frame + 1) * frame_bytes, self.delta):
             self.data.seek(address)
             data.append(unpack('<I', self.data.read(4)))
@@ -101,7 +102,7 @@ class IssFile:
     def get_carpet(self, c, t, min_n_lines=1):
         assert c < self.shape[2] and t < self.shape[4], \
             f'carpet {c = }, {t = } not in shape {self.shape[2]}, {self.shape[4]}'
-        frame = c + (2 * t + 1) * self.shape[2]
+        frame = int(c) + (2 * int(t) + 1) * self.shape[2]
         frame_bytes = self.shape[0] * self.shape[1] * self.delta
         data, metadata = [], []
         self.data.seek(frame * frame_bytes)
diff --git a/setup.py b/setup.py
index e0ba8e5..f0f12cb 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@ with open('README.md', 'r') as fh:
 
 setuptools.setup(
     name='issfile',
-    version='2022.10.3',
+    version='2022.10.4',
     author='Wim Pomp @ Lenstra lab NKI',
     author_email='w.pomp@nki.nl',
     description='Open ISS files.',