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# Copyright 2014 Diamond Light Source Ltd. |
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# |
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# Licensed under the Apache License, Version 2.0 (the "License"); |
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# you may not use this file except in compliance with the License. |
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# You may obtain a copy of the License at |
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# |
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# http://www.apache.org/licenses/LICENSE-2.0 |
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# |
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# Unless required by applicable law or agreed to in writing, software |
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# distributed under the License is distributed on an "AS IS" BASIS, |
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
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# See the License for the specific language governing permissions and |
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# limitations under the License. |
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""" |
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.. module:: mrc_saver |
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:platform: Unix |
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:synopsis: Saves data as .mrc file |
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.. moduleauthor:: Elaine Ho <[email protected]> |
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""" |
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from savu.plugins.utils import register_plugin |
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from savu.plugins.plugin import Plugin |
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# Import any additional libraries or base plugins here. |
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import os |
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import mrcfile |
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import logging |
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from savu.plugins.savers.base_image_saver import BaseImageSaver |
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from savu.plugins.driver.cpu_plugin import CpuPlugin |
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import savu.core.utils as cu |
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# This decorator is required for the configurator to recognise the plugin |
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@register_plugin |
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class MrcSaver(BaseImageSaver, CpuPlugin): |
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# Each class must inherit from the Plugin class and a driver |
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def __init__(self): |
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super(MrcSaver, self).__init__("MrcSaver") |
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self.in_data = None |
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self.out_filename = None |
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def pre_process(self): |
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# Get metadata to create mrc file |
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self.in_data = self.get_in_datasets()[0] |
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self.out_filename = self.__get_file_name() |
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data_type_lookup = {'int8': 0, 'int16': 1, 'float32':2, 'complex64':4, 'uint16':6} |
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try: |
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mrc_mode = data_type_lookup[self.parameters['mrc_mode']] |
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except: |
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msg = "Mrc mode must be one of {}, "\ |
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"defaulting to uint16".format(list(data_type_lookup.keys())) |
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mrc_mode = data_type_lookup['uint16'] |
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logging.warning(msg) |
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cu.user_message(msg) |
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# Create mrc file |
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self.mrc = mrcfile.new_mmap( |
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name=self.out_filename, |
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shape=self.in_data.get_shape(), |
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mrc_mode=mrc_mode, |
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) |
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logging.info("Created mrc file {}".format(self.out_filename)) |
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def process_frames(self, data): |
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# Save data to mrc in parallel |
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idx = self.get_current_slice_list()[0] |
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self.mrc.data[idx] = data[0] |
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logging.debug("Processed frame {}".format(idx[0])) |
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def post_process(self): |
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# Close mrc file |
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self.mrc.close() |
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logging.info("MRC file closed") |
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def __get_file_name(self): |
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# Get the mrc output filename in the format <original_img_name>_processed.mrc |
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out_path = self.exp.meta_data.get('out_path') |
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imgname = os.path.splitext(os.path.split(self.exp.meta_data.get('data_file'))[-1])[0] |
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fname = "{}_processed.mrc".format(imgname) |
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return os.path.join(out_path, fname) |
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DiamondLightSource /
Savu
