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Merge pull request #39 from ggirelli/ggirelli-patch-nd2reader-from-file

Update to reader.py for issue #35
master
Ruben Verweij 4 years ago
committed by GitHub
parent
commit
cbb27ba3cc
No known key found for this signature in database GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 63 additions and 29 deletions
  1. +46
    -21
      nd2reader/reader.py
  2. +17
    -8
      tests/test_reader.py

+ 46
- 21
nd2reader/reader.py View File

@ -11,18 +11,28 @@ class ND2Reader(FramesSequenceND):
This is the main class: use this to process your .nd2 files.
"""
_fh = None
class_priority = 12
def __init__(self, filename):
def __init__(self, fh):
"""
Arguments:
fh {str} -- absolute path to .nd2 file
fh {IO} -- input buffer handler (opened with "rb" mode)
"""
super(ND2Reader, self).__init__()
if not filename.endswith(".nd2"):
raise InvalidFileType("The file %s you want to read with nd2reader does not have extension .nd2." % filename)
if isinstance(fh, str):
if not fh.endswith(".nd2"):
raise InvalidFileType(
("The file %s you want to read with nd2reader" % fh)
+ " does not have extension .nd2."
)
fh = open(fh, "rb")
self.filename = filename
self._fh = fh
self.filename = ""
# first use the parser to parse the file
self._fh = open(filename, "rb")
self._parser = Parser(self._fh)
# Setup metadata
@ -42,7 +52,7 @@ class ND2Reader(FramesSequenceND):
"""Let PIMS open function use this reader for opening .nd2 files
"""
return {'nd2'} | super(ND2Reader, cls).class_exts()
return {"nd2"} | super(ND2Reader, cls).class_exts()
def close(self):
"""Correctly close the file handle
@ -119,22 +129,24 @@ class ND2Reader(FramesSequenceND):
@property
def frame_rate(self):
"""The (average) frame rate
Returns:
float: the (average) frame rate in frames per second
"""
total_duration = 0.0
for loop in self.metadata['experiment']['loops']:
total_duration += loop['duration']
for loop in self.metadata["experiment"]["loops"]:
total_duration += loop["duration"]
if total_duration == 0:
total_duration = self.timesteps[-1]
if total_duration == 0:
raise ValueError('Total measurement duration could not be determined from loops')
raise ValueError(
"Total measurement duration could not be determined from loops"
)
return self.metadata['num_frames'] / (total_duration/1000.0)
return self.metadata["num_frames"] / (total_duration / 1000.0)
def _get_metadata_property(self, key, default=None):
if self.metadata is None:
@ -152,12 +164,22 @@ class ND2Reader(FramesSequenceND):
"""Setup the xyctz axes, iterate over t axis by default
"""
self._init_axis_if_exists('x', self._get_metadata_property("width", default=0))
self._init_axis_if_exists('y', self._get_metadata_property("height", default=0))
self._init_axis_if_exists('c', len(self._get_metadata_property("channels", default=[])), min_size=2)
self._init_axis_if_exists('t', len(self._get_metadata_property("frames", default=[])))
self._init_axis_if_exists('z', len(self._get_metadata_property("z_levels", default=[])), min_size=2)
self._init_axis_if_exists('v', len(self._get_metadata_property("fields_of_view", default=[])), min_size=2)
self._init_axis_if_exists("x", self._get_metadata_property("width", default=0))
self._init_axis_if_exists("y", self._get_metadata_property("height", default=0))
self._init_axis_if_exists(
"c", len(self._get_metadata_property("channels", default=[])), min_size=2
)
self._init_axis_if_exists(
"t", len(self._get_metadata_property("frames", default=[]))
)
self._init_axis_if_exists(
"z", len(self._get_metadata_property("z_levels", default=[])), min_size=2
)
self._init_axis_if_exists(
"v",
len(self._get_metadata_property("fields_of_view", default=[])),
min_size=2,
)
if len(self.sizes) == 0:
raise EmptyFileError("No axes were found for this .nd2 file.")
@ -165,7 +187,7 @@ class ND2Reader(FramesSequenceND):
# provide the default
self.iter_axes = self._guess_default_iter_axis()
self._register_get_frame(self.get_frame_2D, 'yx')
self._register_get_frame(self.get_frame_2D, "yx")
def _init_axis_if_exists(self, axis, size, min_size=1):
if size >= min_size:
@ -177,7 +199,7 @@ class ND2Reader(FramesSequenceND):
Returns:
the axis to iterate over
"""
priority = ['t', 'z', 'c', 'v']
priority = ["t", "z", "c", "v"]
found_axes = []
for axis in priority:
try:
@ -202,6 +224,9 @@ class ND2Reader(FramesSequenceND):
if self._timesteps is not None and len(self._timesteps) > 0:
return self._timesteps
self._timesteps = np.array(list(self._parser._raw_metadata.acquisition_times), dtype=np.float) * 1000.0
self._timesteps = (
np.array(list(self._parser._raw_metadata.acquisition_times), dtype=np.float)
* 1000.0
)
return self._timesteps

+ 17
- 8
tests/test_reader.py View File

@ -16,18 +16,27 @@ class TestReader(unittest.TestCase):
def test_extension(self):
self.assertTrue('nd2' in ND2Reader.class_exts())
def cmp_two_readers(self, r1, r2):
attributes = r1.data['image_attributes']['SLxImageAttributes']
self.assertEqual(r2.metadata['width'], attributes['uiWidth'])
self.assertEqual(r2.metadata['height'], attributes['uiHeight'])
self.assertEqual(r2.metadata['width'], r2.sizes['x'])
self.assertEqual(r2.metadata['height'], r2.sizes['y'])
self.assertEqual(r2.pixel_type, np.float64)
self.assertEqual(r2.iter_axes, ['t'])
def test_init_and_init_axes(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
attributes = artificial.data['image_attributes']['SLxImageAttributes']
self.assertEqual(reader.metadata['width'], attributes['uiWidth'])
self.assertEqual(reader.metadata['height'], attributes['uiHeight'])
self.cmp_two_readers(artificial, reader)
self.assertEqual(reader.metadata['width'], reader.sizes['x'])
self.assertEqual(reader.metadata['height'], reader.sizes['y'])
self.assertEqual(reader.pixel_type, np.float64)
self.assertEqual(reader.iter_axes, ['t'])
def test_init_from_handler(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
with open('test_data/test_nd2_reader.nd2', "rb") as FH:
with ND2Reader(FH) as reader:
self.cmp_two_readers(artificial, reader)
def test_init_empty_file(self):
with ArtificialND2('test_data/empty.nd2', skip_blocks=['label_map_marker']):


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