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zolfa-nd2reader
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Extend artificial to also write the label_map + data to file for more extensive unit testing

feature/load_slices
Ruben Verweij 7 years ago
parent
6128ba4838
commit
9f3e4c1b35
4 changed files with 166 additions and 55 deletions
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  1. +140
    -42
      nd2reader/artificial.py
  2. +18
    -3
      nd2reader/raw_metadata.py
  3. +2
    -1
      tests/test_label_map.py
  4. +6
    -9
      tests/test_raw_metadata.py

+ 140
- 42
nd2reader/artificial.py View File

@ -3,15 +3,22 @@
import six
import numpy as np
import struct
from nd2reader.common import check_or_make_dir
from os import path
class ArtificialND2(object):
"""Artificial ND2 class (for testing purposes)
"""
header = 0xabeceda
relative_offset = 0
def __init__(self, file, version=(3, 0)):
self._fh = open(file, 'wb')
self.write_version(version)
self.version = version
self.raw_text, self.locations, self.data = None, None, None
check_or_make_dir(path.dirname(file))
self._fh = open(file, 'w+b', 0)
self.write_file()
def __enter__(self):
return self
@ -35,18 +42,32 @@ class ArtificialND2(object):
if self._fh is not None:
self._fh.close()
def write_version(self, version=(3, 0)):
def write_file(self):
self.write_version()
self.raw_text, self.locations, self.data = self.write_label_map()
def write_version(self):
"""Write file header
"""
# write 16 empty bytes
self._fh.write(bytearray(16))
# write version info
version_info = six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver%s.%s' % version)
self._fh.write(version_info)
self._fh.write(self._get_version_string())
def _get_version_string(self):
return six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver%s.%s' % self.version)
def _get_version_byte_length(self):
return 16 + len(self._get_version_string())
def write_label_map(self):
raw_text, locations, data = self.create_label_map_bytes()
self._fh.write(raw_text)
@staticmethod
def create_label_map_bytes():
return raw_text, locations, data
def create_label_map_bytes(self):
"""Construct a binary label map
Returns:
@ -54,40 +75,117 @@ class ArtificialND2(object):
"""
raw_text = six.b('')
labels = {
'image_attributes': "ImageAttributesLV!",
'image_text_info': "ImageTextInfoLV!",
'image_metadata': "ImageMetadataLV!",
'image_metadata_sequence': "ImageMetadataSeqLV|0!",
'image_calibration': "ImageCalibrationLV|0!",
'x_data': "CustomData|X!",
'y_data': "CustomData|Y!",
'z_data': "CustomData|Z!",
'roi_metadata': "CustomData|RoiMetadata_v1!",
'pfs_status': "CustomData|PFS_STATUS!",
'pfs_offset': "CustomData|PFS_OFFSET!",
'guid': "CustomData|GUIDStore!",
'description': "CustomData|CustomDescriptionV1_0!",
'camera_exposure_time': "CustomData|Camera_ExposureTime1!",
'camera_temp': "CustomData|CameraTemp1!",
'acquisition_times': "CustomData|AcqTimesCache!",
'acquisition_times_2': "CustomData|AcqTimes2Cache!",
'acquisition_frames': "CustomData|AcqFramesCache!",
'lut_data': "CustomDataVar|LUTDataV1_0!",
'grabber_settings': "CustomDataVar|GrabberCameraSettingsV1_0!",
'custom_data': "CustomDataVar|CustomDataV2_0!",
'app_info': "CustomDataVar|AppInfo_V1_0!",
'image_frame_0': "ImageDataSeq|0!"
}
data = {}
labels = [
'image_attributes',
'image_text_info',
'image_metadata',
'image_metadata_sequence',
'image_calibration',
'x_data',
'y_data',
'z_data',
'roi_metadata',
'pfs_status',
'pfs_offset',
'guid',
'description',
'camera_exposure_time',
'camera_temp',
'acquisition_times',
'acquisition_times_2',
'acquisition_frames',
'lut_data',
'grabber_settings',
'custom_data',
'app_info',
'image_frame_0'
]
file_labels = [
"ImageAttributesLV!",
"ImageTextInfoLV!",
"ImageMetadataLV!",
"ImageMetadataSeqLV|0!",
"ImageCalibrationLV|0!",
"CustomData|X!",
"CustomData|Y!",
"CustomData|Z!",
"CustomData|RoiMetadata_v1!",
"CustomData|PFS_STATUS!",
"CustomData|PFS_OFFSET!",
"CustomData|GUIDStore!",
"CustomData|CustomDescriptionV1_0!",
"CustomData|Camera_ExposureTime1!",
"CustomData|CameraTemp1!",
"CustomData|AcqTimesCache!",
"CustomData|AcqTimes2Cache!",
"CustomData|AcqFramesCache!",
"CustomDataVar|LUTDataV1_0!",
"CustomDataVar|GrabberCameraSettingsV1_0!",
"CustomDataVar|CustomDataV2_0!",
"CustomDataVar|AppInfo_V1_0!",
"ImageDataSeq|0!"
]
file_data, file_data_dict = self._get_file_data(labels)
locations = {}
# generate random positions and lengths
lengths = np.random.random_integers(1, 999, len(labels))
positions = np.subtract(np.cumsum(lengths), lengths[0])
for length, pos, label in zip(lengths, positions, labels):
raw_text += six.b(labels[label])
raw_text += struct.pack('QQ', pos, length)
data[label] = (pos, length)
return raw_text, data
version_length = self._get_version_byte_length()
# calculate data length
label_length = np.sum([len(six.b(l)) + 16 for l in file_labels])
# write label map
cur_pos = version_length + label_length
for label, file_label, data in zip(labels, file_labels, file_data):
raw_text += six.b(file_label)
data_length = len(data)
raw_text += struct.pack('QQ', cur_pos, data_length)
locations[label] = (cur_pos, data_length)
cur_pos += data_length
# write data
raw_text += six.b('').join(file_data)
return raw_text, locations, file_data_dict
def _pack_data_with_metadata(self, data):
data = struct.pack('I', data)
raw_data = struct.pack("IIQ", self.header, self.relative_offset, len(data))
raw_data += data
return raw_data
def _get_file_data(self, labels):
file_data = [
7, # ImageAttributesLV!",
7, # ImageTextInfoLV!",
7, # ImageMetadataLV!",
7, # ImageMetadataSeqLV|0!",
7, # ImageCalibrationLV|0!",
7, # CustomData|X!",
7, # CustomData|Y!",
7, # CustomData|Z!",
7, # CustomData|RoiMetadata_v1!",
7, # CustomData|PFS_STATUS!",
7, # CustomData|PFS_OFFSET!",
7, # CustomData|GUIDStore!",
7, # CustomData|CustomDescriptionV1_0!",
7, # CustomData|Camera_ExposureTime1!",
7, # CustomData|CameraTemp1!",
7, # CustomData|AcqTimesCache!",
7, # CustomData|AcqTimes2Cache!",
7, # CustomData|AcqFramesCache!",
7, # CustomDataVar|LUTDataV1_0!",
7, # CustomDataVar|GrabberCameraSettingsV1_0!",
7, # CustomDataVar|CustomDataV2_0!",
7, # CustomDataVar|AppInfo_V1_0!",
7, # ImageDataSeq|0!"
]
file_data_dict = {l: d for l, d in zip(labels, file_data)}
# convert to bytes
file_data = [self._pack_data_with_metadata(d) for d in file_data]
return file_data, file_data_dict

+ 18
- 3
nd2reader/raw_metadata.py View File

@ -383,9 +383,24 @@ class RawMetadata(object):
interval = get_from_dict_if_exists('dAvgPeriodDiff', loop)
if interval is None or interval <= 0:
# In some cases, both keys are not saved. Then try to calculate it.
number_of_loops = get_from_dict_if_exists('uiCount', loop)
number_of_loops = number_of_loops if number_of_loops is not None and number_of_loops > 0 else 1
interval = duration / number_of_loops
interval = RawMetadata._guess_sampling_from_loops(duration, loop)
return interval
@staticmethod
def _guess_sampling_from_loops(duration, loop):
""" In some cases, both keys are not saved. Then try to calculate it.
Args:
duration: the total duration of the loop
loop: the raw loop data
Returns:
float: the guessed sampling interval in milliseconds
"""
number_of_loops = get_from_dict_if_exists('uiCount', loop)
number_of_loops = number_of_loops if number_of_loops is not None and number_of_loops > 0 else 1
interval = duration / number_of_loops
return interval
@property


+ 2
- 1
tests/test_label_map.py View File

@ -5,7 +5,8 @@ from nd2reader.artificial import ArtificialND2
class TestLabelMap(unittest.TestCase):
def setUp(self):
self.raw_text, self.locations = ArtificialND2.create_label_map_bytes()
self.nd2 = ArtificialND2('test_data/test_nd2_label_map001.nd2')
self.raw_text, self.locations = self.nd2.raw_text, self.nd2.locations
self.label_map = LabelMap(self.raw_text)
def test_image_data_location(self):


+ 6
- 9
tests/test_raw_metadata.py View File

@ -6,11 +6,11 @@ from nd2reader.raw_metadata import RawMetadata
class TestRawMetadata(unittest.TestCase):
def setUp(self):
self.raw_text, self.locations = ArtificialND2.create_label_map_bytes()
self.nd2 = ArtificialND2('test_data/test_nd2_raw_metadata001.nd2')
self.raw_text, self.locations, self.file_data = self.nd2.raw_text, self.nd2.locations, self.nd2.data
self.label_map = LabelMap(self.raw_text)
self.metadata = RawMetadata(None, self.label_map)
self.metadata = RawMetadata(self.nd2.file_handle, self.label_map)
def test_parse_roi_shape(self):
self.assertEqual(self.metadata._parse_roi_shape(3), 'rectangle')
@ -26,7 +26,7 @@ class TestRawMetadata(unittest.TestCase):
def test_dict(self):
self.assertTrue(type(self.metadata.__dict__) is dict)
def test_parsed_metadata(self):
def test_parsed_metadata_has_all_keys(self):
metadata = self.metadata.get_parsed_metadata()
self.assertTrue(type(metadata) is dict)
required_keys = ["height", "width", "date", "fields_of_view", "frames", "z_levels", "total_images_per_channel",
@ -34,8 +34,5 @@ class TestRawMetadata(unittest.TestCase):
for required in required_keys:
self.assertTrue(required in metadata)
# it should now be stored, see if that dict is returned
metadata['height'] = 1
self.metadata._metadata_parsed['height'] = 1
second_metadata = self.metadata.get_parsed_metadata()
self.assertDictEqual(metadata, second_metadata)
def test_pfs_status(self):
self.assertEqual(self.file_data['pfs_status'], self.metadata.pfs_status[0])

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