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191 lines
5.7 KiB
191 lines
5.7 KiB
"""Functions to create artificial nd2 data for testing purposes
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"""
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import six
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import numpy as np
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import struct
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from nd2reader.common import check_or_make_dir
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from os import path
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class ArtificialND2(object):
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"""Artificial ND2 class (for testing purposes)
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"""
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header = 0xabeceda
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relative_offset = 0
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def __init__(self, file, version=(3, 0)):
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self.version = version
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self.raw_text, self.locations, self.data = None, None, None
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check_or_make_dir(path.dirname(file))
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self._fh = open(file, 'w+b', 0)
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self.write_file()
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def __enter__(self):
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return self
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def __exit__(self, exc_type, exc_value, traceback):
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self.close()
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@property
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def file_handle(self):
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"""The file handle to the binary file
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Returns:
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file: the file handle
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"""
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return self._fh
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def close(self):
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"""Correctly close the file handle
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"""
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if self._fh is not None:
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self._fh.close()
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def write_file(self):
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self.write_version()
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self.raw_text, self.locations, self.data = self.write_label_map()
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def write_version(self):
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"""Write file header
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"""
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# write 16 empty bytes
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self._fh.write(bytearray(16))
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# write version info
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self._fh.write(self._get_version_string())
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def _get_version_string(self):
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return six.b('ND2 FILE SIGNATURE CHUNK NAME01!Ver%s.%s' % self.version)
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def _get_version_byte_length(self):
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return 16 + len(self._get_version_string())
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def write_label_map(self):
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raw_text, locations, data = self.create_label_map_bytes()
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self._fh.write(raw_text)
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return raw_text, locations, data
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def create_label_map_bytes(self):
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"""Construct a binary label map
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Returns:
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tuple: (binary data, dictionary data)
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"""
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raw_text = six.b('')
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labels = [
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'image_attributes',
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'image_text_info',
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'image_metadata',
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'image_metadata_sequence',
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'image_calibration',
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'x_data',
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'y_data',
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'z_data',
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'roi_metadata',
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'pfs_status',
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'pfs_offset',
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'guid',
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'description',
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'camera_exposure_time',
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'camera_temp',
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'acquisition_times',
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'acquisition_times_2',
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'acquisition_frames',
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'lut_data',
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'grabber_settings',
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'custom_data',
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'app_info',
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'image_frame_0'
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]
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file_labels = [
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"ImageAttributesLV!",
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"ImageTextInfoLV!",
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"ImageMetadataLV!",
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"ImageMetadataSeqLV|0!",
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"ImageCalibrationLV|0!",
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"CustomData|X!",
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"CustomData|Y!",
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"CustomData|Z!",
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"CustomData|RoiMetadata_v1!",
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"CustomData|PFS_STATUS!",
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"CustomData|PFS_OFFSET!",
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"CustomData|GUIDStore!",
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"CustomData|CustomDescriptionV1_0!",
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"CustomData|Camera_ExposureTime1!",
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"CustomData|CameraTemp1!",
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"CustomData|AcqTimesCache!",
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"CustomData|AcqTimes2Cache!",
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"CustomData|AcqFramesCache!",
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"CustomDataVar|LUTDataV1_0!",
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"CustomDataVar|GrabberCameraSettingsV1_0!",
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"CustomDataVar|CustomDataV2_0!",
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"CustomDataVar|AppInfo_V1_0!",
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"ImageDataSeq|0!"
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]
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file_data, file_data_dict = self._get_file_data(labels)
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locations = {}
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# generate random positions and lengths
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version_length = self._get_version_byte_length()
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# calculate data length
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label_length = np.sum([len(six.b(l)) + 16 for l in file_labels])
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# write label map
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cur_pos = version_length + label_length
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for label, file_label, data in zip(labels, file_labels, file_data):
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raw_text += six.b(file_label)
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data_length = len(data)
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raw_text += struct.pack('QQ', cur_pos, data_length)
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locations[label] = (cur_pos, data_length)
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cur_pos += data_length
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# write data
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raw_text += six.b('').join(file_data)
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return raw_text, locations, file_data_dict
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def _pack_data_with_metadata(self, data):
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data = struct.pack('I', data)
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raw_data = struct.pack("IIQ", self.header, self.relative_offset, len(data))
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raw_data += data
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return raw_data
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def _get_file_data(self, labels):
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file_data = [
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7, # ImageAttributesLV!",
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7, # ImageTextInfoLV!",
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7, # ImageMetadataLV!",
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7, # ImageMetadataSeqLV|0!",
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7, # ImageCalibrationLV|0!",
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7, # CustomData|X!",
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7, # CustomData|Y!",
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7, # CustomData|Z!",
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7, # CustomData|RoiMetadata_v1!",
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7, # CustomData|PFS_STATUS!",
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7, # CustomData|PFS_OFFSET!",
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7, # CustomData|GUIDStore!",
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7, # CustomData|CustomDescriptionV1_0!",
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7, # CustomData|Camera_ExposureTime1!",
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7, # CustomData|CameraTemp1!",
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7, # CustomData|AcqTimesCache!",
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7, # CustomData|AcqTimes2Cache!",
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7, # CustomData|AcqFramesCache!",
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7, # CustomDataVar|LUTDataV1_0!",
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7, # CustomDataVar|GrabberCameraSettingsV1_0!",
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7, # CustomDataVar|CustomDataV2_0!",
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7, # CustomDataVar|AppInfo_V1_0!",
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7, # ImageDataSeq|0!"
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]
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file_data_dict = {l: d for l, d in zip(labels, file_data)}
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# convert to bytes
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file_data = [self._pack_data_with_metadata(d) for d in file_data]
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return file_data, file_data_dict
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