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fix mrc import axes #52

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merged 3 commits into from
Apr 29, 2022
Merged

fix mrc import axes #52

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e92a27b
fix mrc import axes
martinschorb Apr 8, 2022
85a8430
Merge branch 'constantinpape:master' into master
martinschorb Apr 27, 2022
ad54d55
make 2D compatible, update test date generation
Apr 28, 2022
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9 changes: 8 additions & 1 deletion elf/io/mrc_wrapper.py
100644 → 100755
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
from collections.abc import Mapping
import numpy as np

try:
import mrcfile
except ImportError:
Expand All @@ -7,7 +9,11 @@

class MRCDataset:
def __init__(self, data_object):
self._data = data_object
im = data_object
# need to swap and flip to meet axes conventions
data0 = np.swapaxes(im, 0, -1)
data1 = np.fliplr(data0)
self._data = np.swapaxes(data1, 0, -1)

@property
def dtype(self):
Expand Down Expand Up @@ -42,6 +48,7 @@ def attrs(self):
class MRCFile(Mapping):
""" Wrapper for an mrc file
"""

def __init__(self, path, mode='r'):
self.path = path
self.mode = mode
Expand Down
11 changes: 8 additions & 3 deletions test/io_tests/test_mrc_wrapper.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -17,14 +17,19 @@ class TestMrcWrapper(unittest.TestCase):

def setUp(self):
os.makedirs(self.tmp_dir)
shape = (64, 64, 64)
shape = (16, 32, 64)
self.data = np.random.rand(*shape).astype('float32')

# change axes order to fit MRC convention
data0 = np.swapaxes(self.data, 0, -1)
data1 = np.fliplr(data0)
out_data = np.swapaxes(data1, 0, -1)

with mrcfile.new(self.out) as f:
f.set_data(self.data)
f.set_data(out_data)

with mrcfile.new(self.out_compressed, compression='gzip') as f:
f.set_data(self.data)
f.set_data(out_data)

def tearDown(self):
rmtree(self.tmp_dir)
Expand Down