From 570404b0cfaeecf4a23034b067fef82f60208ef2 Mon Sep 17 00:00:00 2001
From: s184058 <s184058@student.dtu.dk>
Date: Wed, 24 Jan 2024 14:48:36 +0100
Subject: [PATCH] Load bigtiff
---
qim3d/io/load.py | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index 4d67274d..49736eb3 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -66,10 +66,14 @@ class DataLoader:
If 'self.virtual_stack' is True, returns a numpy.memmap object.
"""
+ # Get the number of TIFF series (some BigTIFF have multiple series)
+ with tifffile.TiffFile(path) as tif:
+ series = len(tif.series)
+
if self.virtual_stack:
vol = tifffile.memmap(path)
else:
- vol = tifffile.imread(path)
+ vol = tifffile.imread(path, key=range(series) if series>1 else None)
log.info("Loaded shape: %s", vol.shape)
@@ -215,7 +219,7 @@ class DataLoader:
"""Load a TXRM/XRM/TXM file from the specified path.
Args:
- path (str): The path to the HDF5 file.
+ path (str): The path to the TXRM/XRM/TXM file.
Returns:
numpy.ndarray or tuple: The loaded volume.
@@ -412,7 +416,7 @@ def load(
log_memory_info(data)
else:
# Only log if file type is not a np.ndarray, i.e., it is some kind of memmap object
- if not isinstance( data[0] if isinstance(data,tuple) else data, np.ndarray ):
+ if not isinstance( type(data[0]) if isinstance(data,tuple) else type(data), np.ndarray ):
log.info("Using virtual stack")
else:
log.warning('Virtual stack is not supported for this file format')
--
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