DiamondLightSource /
Savu
| @@ 385-418 (lines=34) @@ | ||
| 382 | for name in datasets: |
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| 383 | self.exp.index['in_data'][name].meta_data.set(key, value) |
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| 384 | ||
| 385 | def setup(self): |
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| 386 | self.exp.log(self.name + " Start calculating center of rotation") |
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| 387 | # set up the output dataset that is created by the plugin |
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| 388 | in_dataset, out_dataset = self.get_datasets() |
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| 389 | in_pData, out_pData = self.get_plugin_datasets() |
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| 390 | in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames()) |
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| 391 | slice_dirs = list(in_dataset[0].get_slice_dimensions()) |
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| 392 | self.orig_full_shape = in_dataset[0].get_shape() |
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| 393 | ||
| 394 | # reduce the data as per data_subset parameter |
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| 395 | self.set_preview(in_dataset[0], self.parameters['preview']) |
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| 396 | total_frames = \ |
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| 397 | self._calc_total_frames(in_dataset[0].get_preview(), slice_dirs) |
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| 398 | ||
| 399 | # copy all required information from in_dataset[0] |
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| 400 | fullData = in_dataset[0] |
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| 401 | new_shape = (np.prod(np.array(fullData.get_shape())[slice_dirs]), 1) |
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| 402 | self.orig_shape = \ |
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| 403 | (np.prod(np.array(self.orig_full_shape)[slice_dirs]), 1) |
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| 404 | out_dataset[0].create_dataset(shape=new_shape, |
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| 405 | axis_labels=['x.pixels', 'y.pixels'], |
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| 406 | remove=True, |
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| 407 | transport='hdf5') |
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| 408 | out_dataset[0].add_pattern("METADATA", core_dims=(1,), slice_dims=(0,)) |
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| 409 | ||
| 410 | out_dataset[1].create_dataset(shape=self.orig_shape, |
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| 411 | axis_labels=['x.pixels', 'y.pixels'], |
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| 412 | remove=True, |
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| 413 | transport='hdf5') |
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| 414 | out_dataset[1].add_pattern("METADATA", core_dims=(1,), slice_dims=(0,)) |
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| 415 | out_pData[0].plugin_data_setup('METADATA', self.get_max_frames()) |
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| 416 | out_pData[1].plugin_data_setup('METADATA', self.get_max_frames()) |
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| 417 | out_pData[1].meta_data.set('fix_total_frames', total_frames) |
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| 418 | self.exp.log(self.name + " End") |
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| 419 | ||
| 420 | def _calc_total_frames(self, preview, slice_dims): |
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| 421 | starts, stops, steps, _ = preview.get_starts_stops_steps() |
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| @@ 265-298 (lines=34) @@ | ||
| 262 | for name in datasets: |
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| 263 | self.exp.index['in_data'][name].meta_data.set(key, value) |
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| 264 | ||
| 265 | def setup(self): |
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| 266 | self.exp.log(self.name + " Start calculating center of rotation") |
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| 267 | # set up the output dataset that is created by the plugin |
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| 268 | in_dataset, out_dataset = self.get_datasets() |
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| 269 | in_pData, out_pData = self.get_plugin_datasets() |
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| 270 | in_pData[0].plugin_data_setup('SINOGRAM', self.get_max_frames()) |
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| 271 | slice_dirs = list(in_dataset[0].get_slice_dimensions()) |
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| 272 | self.orig_full_shape = in_dataset[0].get_shape() |
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| 273 | ||
| 274 | # reduce the data as per data_subset parameter |
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| 275 | self.set_preview(in_dataset[0], self.parameters['preview']) |
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| 276 | total_frames = \ |
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| 277 | self._calc_total_frames(in_dataset[0].get_preview(), slice_dirs) |
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| 278 | ||
| 279 | # copy all required information from in_dataset[0] |
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| 280 | fullData = in_dataset[0] |
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| 281 | new_shape = (np.prod(np.array(fullData.get_shape())[slice_dirs]), 1) |
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| 282 | self.orig_shape = \ |
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| 283 | (np.prod(np.array(self.orig_full_shape)[slice_dirs]), 1) |
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| 284 | out_dataset[0].create_dataset(shape=new_shape, |
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| 285 | axis_labels=['x.pixels', 'y.pixels'], |
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| 286 | remove=True, |
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| 287 | transport='hdf5') |
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| 288 | out_dataset[0].add_pattern("METADATA", core_dims=(1,), slice_dims=(0,)) |
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| 289 | ||
| 290 | out_dataset[1].create_dataset(shape=self.orig_shape, |
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| 291 | axis_labels=['x.pixels', 'y.pixels'], |
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| 292 | remove=True, |
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| 293 | transport='hdf5') |
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| 294 | out_dataset[1].add_pattern("METADATA", core_dims=(1,), slice_dims=(0,)) |
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| 295 | out_pData[0].plugin_data_setup('METADATA', self.get_max_frames()) |
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| 296 | out_pData[1].plugin_data_setup('METADATA', self.get_max_frames()) |
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| 297 | out_pData[1].meta_data.set('fix_total_frames', total_frames) |
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| 298 | self.exp.log(self.name + " End") |
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| 299 | ||
| 300 | def _calc_total_frames(self, preview, slice_dims): |
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| 301 | starts, stops, steps, _ = preview.get_starts_stops_steps() |
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