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280 lines
9.7 KiB
280 lines
9.7 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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global_labels = ['image_attributes', 'image_text_info', 'image_metadata',
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'image_metadata_sequence', 'image_calibration', 'x_data',
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'y_data', 'z_data', 'roi_metadata', 'pfs_status', 'pfs_offset',
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'guid', 'description', 'camera_exposure_time', 'camera_temp',
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'acquisition_times', 'acquisition_times_2',
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'acquisition_frames', 'lut_data', 'grabber_settings',
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'custom_data', 'app_info', 'image_frame_0']
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global_file_labels = ["ImageAttributesLV!", "ImageTextInfoLV!",
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"ImageMetadataLV!", "ImageMetadataSeqLV|0!",
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"ImageCalibrationLV|0!", "CustomData|X!", "CustomData|Y!",
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"CustomData|Z!", "CustomData|RoiMetadata_v1!",
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"CustomData|PFS_STATUS!", "CustomData|PFS_OFFSET!",
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"CustomData|GUIDStore!", "CustomData|CustomDescriptionV1_0!",
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"CustomData|Camera_ExposureTime1!", "CustomData|CameraTemp1!",
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"CustomData|AcqTimesCache!", "CustomData|AcqTimes2Cache!",
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"CustomData|AcqFramesCache!", "CustomDataVar|LUTDataV1_0!",
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"CustomDataVar|GrabberCameraSettingsV1_0!",
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"CustomDataVar|CustomDataV2_0!", "CustomDataVar|AppInfo_V1_0!",
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"ImageDataSeq|0!"]
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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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data_types = {'unsigned_char': 1,
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'unsigned_int': 2,
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'unsigned_int_2': 3,
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'unsigned_long': 5,
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'double': 6,
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'string': 8,
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'char_array': 9,
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'metadata_item': 11,
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}
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def __init__(self, file, version=(3, 0), skip_blocks=None):
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self.version = version
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self.raw_text, self.locations, self.data = b'', 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(skip_blocks)
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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, skip_blocks=None):
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if skip_blocks is None:
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skip_blocks = []
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if 'version' not in skip_blocks:
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# write version header at start of the file
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self.write_version()
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if 'label_map' not in skip_blocks:
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# write label map + data in the center
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self.locations, self.data = self.write_label_map()
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if 'label_map_marker' not in skip_blocks:
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# write start position of label map at the end of the file
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self.write_label_map_info()
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# write all to file
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self._fh.write(self.raw_text)
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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.raw_text += bytearray(16)
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# write version info
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self.raw_text += self._get_version_string()
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def write_label_map_info(self):
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"""Write the location of the start of the label map at the end of the file
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"""
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location = self._get_version_byte_length()
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self.raw_text += struct.pack("Q", location)
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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.raw_text += raw_text
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return 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 = global_labels
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file_labels = global_file_labels
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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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packed_data = self._pack_raw_data_with_metadata(data)
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raw_data = struct.pack("IIQ", self.header, self.relative_offset, len(packed_data))
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raw_data += packed_data
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return raw_data
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def _pack_raw_data_with_metadata(self, data):
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raw_data = b''
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if isinstance(data, dict):
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raw_data = self._pack_dict_with_metadata(data)
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elif isinstance(data, int):
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raw_data = struct.pack('I', data)
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elif isinstance(data, float):
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raw_data = struct.pack('d', data)
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elif isinstance(data, str):
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raw_data = self._str_to_padded_bytes(data)
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return raw_data
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def _get_data_type(self, data):
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if isinstance(data, dict):
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return self.data_types['metadata_item']
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elif isinstance(data, int):
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return self.data_types['unsigned_int']
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elif isinstance(data, str):
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return self.data_types['string']
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else:
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return self.data_types['double']
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@staticmethod
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def _str_to_padded_bytes(data):
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return six.b('').join([struct.pack('cx', six.b(s)) for s in data]) + struct.pack('xx')
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def _pack_dict_with_metadata(self, data):
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raw_data = b''
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for data_key in data.keys():
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# names have always one character extra and are padded in zero bytes???
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b_data_key = self._str_to_padded_bytes(data_key)
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# header consists of data type and length of key name, it is represented by 2 unsigned chars
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raw_data += struct.pack('BB', self._get_data_type(data[data_key]), len(data_key) + 1)
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raw_data += b_data_key
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sub_data = self._pack_raw_data_with_metadata(data[data_key])
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if isinstance(data[data_key], dict):
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# Pack: the number of keys and the length of raw data until now, sub data
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# and the 12 bytes that we add now
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raw_data += struct.pack("<IQ", len(data[data_key].keys()), len(sub_data) + len(raw_data) + 12)
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raw_data += sub_data
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if isinstance(data[data_key], dict):
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# apparently there is also a huge empty space
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raw_data += b''.join([struct.pack('x')] * len(data[data_key].keys()) * 8)
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return raw_data
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@staticmethod
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def _get_slx_img_attrib():
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return {'uiWidth': 128,
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'uiWidthBytes': 256,
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'uiHeight': 128,
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'uiComp': 1,
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'uiBpcInMemory': 16,
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'uiBpcSignificant': 12,
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'uiSequenceCount': 70,
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'uiTileWidth': 128,
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'uiTileHeight': 128,
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'eCompression': 2,
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'dCompressionParam': -1.0,
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'ePixelType': 1,
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'uiVirtualComponents': 1
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}
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@staticmethod
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def _get_slx_picture_metadata():
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return {'sPicturePlanes':
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{
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'sPlaneNew': {
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# channels are numbered a0, a1, ..., aN
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'a0': {
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'sDescription': 'TRITC'
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}
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}
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}
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}
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def _get_file_data(self, labels):
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file_data = [
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{'SLxImageAttributes': self._get_slx_img_attrib()}, # ImageAttributesLV!",
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7, # ImageTextInfoLV!",
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7, # ImageMetadataLV!",
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{'SLxPictureMetadata': self._get_slx_picture_metadata()}, # 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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[0], # CustomData|AcqTimesCache!",
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[0], # CustomData|AcqTimes2Cache!",
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[0], # 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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