"""Functions to create artificial nd2 data for testing purposes """ 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.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 def __exit__(self, exc_type, exc_value, traceback): self.close() @property def file_handle(self): """The file handle to the binary file Returns: file: the file handle """ return self._fh def close(self): """Correctly close the file handle """ if self._fh is not None: self._fh.close() 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 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) return raw_text, locations, data def create_label_map_bytes(self): """Construct a binary label map Returns: tuple: (binary data, dictionary data) """ raw_text = six.b('') 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 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