Mercurial > repos > muon-spectroscopy-computational-project > larch_athena

comparison larch_athena.py @ 4:a0d3b0fe0fa3 draft

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
author muon-spectroscopy-computational-project
date Thu, 11 Apr 2024 09:01:59 +0000
parents 82e9dd980916
children 27015eaf9a78
comparison
equal deleted inserted replaced
3:82e9dd980916 4:a0d3b0fe0fa3
259 do_calibrate: bool, 259 do_calibrate: bool,
260 calibrate_settings: dict, 260 calibrate_settings: dict,
261 do_rebin: bool, 261 do_rebin: bool,
262 do_pre_edge: bool, 262 do_pre_edge: bool,
263 pre_edge_settings: dict, 263 pre_edge_settings: dict,
264 ref_channel: str,
264 do_xftf: bool, 265 do_xftf: bool,
265 xftf_settings: dict, 266 xftf_settings: dict,
266 plot_graph: list, 267 plot_graph: list,
267 annotation: str, 268 annotation: str,
268 path_key: str = "out", 269 path_key: str = "out",
284 xas_data = xas_data.rebinned 285 xas_data = xas_data.rebinned
285 # After re-bin, will need to redo pre-edge 286 # After re-bin, will need to redo pre-edge
286 do_pre_edge = True 287 do_pre_edge = True
287 288
288 if do_pre_edge: 289 if do_pre_edge:
289 pre_edge_with_defaults(xas_data, pre_edge_settings) 290 pre_edge_with_defaults(xas_data, pre_edge_settings, ref_channel)
290 291
291 if do_xftf: 292 if do_xftf:
292 xftf_with_defaults(xas_data, xftf_settings) 293 xftf_with_defaults(xas_data, xftf_settings)
293 294
294 if plot_graph: 295 if plot_graph:
320 if "edge" in plot_keys: 321 if "edge" in plot_keys:
321 plt.subplot(nrows, 1, index) 322 plt.subplot(nrows, 1, index)
322 plt.plot(xas_data.energy, xas_data.pre_edge, "g", label="pre-edge") 323 plt.plot(xas_data.energy, xas_data.pre_edge, "g", label="pre-edge")
323 plt.plot(xas_data.energy, xas_data.post_edge, "r", label="post-edge") 324 plt.plot(xas_data.energy, xas_data.post_edge, "r", label="post-edge")
324 plt.plot(xas_data.energy, xas_data.mu, "b", label="fit data") 325 plt.plot(xas_data.energy, xas_data.mu, "b", label="fit data")
326 if hasattr(xas_data, "mu_std"):
327 plt.fill_between(
328 x=xas_data.energy,
329 y1=xas_data.mu - xas_data.mu_std,
330 y2=xas_data.mu + xas_data.mu_std,
331 alpha=0.2,
332 label="standard deviation",
333 )
334 e0 = xas_data.e0
335 plt.axvline(e0, color="m", label=f"edge energy = {e0}")
325 plt.grid(color="r", linestyle=":", linewidth=1) 336 plt.grid(color="r", linestyle=":", linewidth=1)
326 plt.xlabel("Energy (eV)") 337 plt.xlabel("Energy (eV)")
327 plt.ylabel("x$\mu$(E)") # noqa: W605 338 plt.ylabel("x$\mu$(E)") # noqa: W605
328 plt.title("Pre-edge and post_edge fitting to $\mu$") # noqa: W605 339 plt.title("Pre-edge and post_edge fitting to $\mu$") # noqa: W605
329 plt.legend() 340 plt.legend()
330 index += 1 341 index += 1
331 342
332 if "flat" in plot_keys: 343 if "flat" in plot_keys:
333 plt.subplot(nrows, 1, index) 344 plt.subplot(nrows, 1, index)
334 plt.plot(xas_data.energy, xas_data.flat) 345 plt.plot(xas_data.energy, xas_data.flat, label="flattened signal")
346 if hasattr(xas_data, "mu_std"):
347 mu_std_normalised = xas_data.mu_std / xas_data.edge_step
348 plt.fill_between(
349 x=xas_data.energy,
350 y1=xas_data.flat - mu_std_normalised,
351 y2=xas_data.flat + mu_std_normalised,
352 alpha=0.2,
353 label="standard deviation",
354 )
355 plt.legend()
335 plt.grid(color="r", linestyle=":", linewidth=1) 356 plt.grid(color="r", linestyle=":", linewidth=1)
336 plt.xlabel("Energy (eV)") 357 plt.xlabel("Energy (eV)")
337 plt.ylabel("Flattened x$\mu$(E)") # noqa: W605 358 plt.ylabel("Flattened x$\mu$(E)") # noqa: W605
338 index += 1 359 index += 1
339 360
355 matplotlib.use("Agg") 376 matplotlib.use("Agg")
356 377
357 dat_file = sys.argv[1] 378 dat_file = sys.argv[1]
358 input_values = json.load(open(sys.argv[2], "r", encoding="utf-8")) 379 input_values = json.load(open(sys.argv[2], "r", encoding="utf-8"))
359 merge_inputs = input_values["merge_inputs"]["merge_inputs"] 380 merge_inputs = input_values["merge_inputs"]["merge_inputs"]
360 data_format = input_values["merge_inputs"]["format"]["format"] 381 format_inputs = input_values["merge_inputs"]["format"]
361 if "is_zipped" in input_values["merge_inputs"]["format"]: 382 if "is_zipped" in format_inputs:
362 is_zipped = bool( 383 is_zipped = bool(format_inputs["is_zipped"]["is_zipped"])
363 input_values["merge_inputs"]["format"]["is_zipped"]["is_zipped"]
364 )
365 else: 384 else:
366 is_zipped = False 385 is_zipped = False
367 386
368 extract_group = None 387 extract_group = None
369 if "extract_group" in input_values["merge_inputs"]["format"]: 388 if "extract_group" in format_inputs:
370 extract_group = input_values["merge_inputs"]["format"]["extract_group"] 389 extract_group = format_inputs["extract_group"]
371 390
372 energy_column = None 391 if "energy_column" not in format_inputs:
373 mu_column = None 392 energy_column = None
374 if "energy_column" in input_values["merge_inputs"]["format"]: 393 else:
375 energy_column = input_values["merge_inputs"]["format"]["energy_column"] 394 energy_column = format_inputs["energy_column"]["energy_column"]
376 if "mu_column" in input_values["merge_inputs"]["format"]: 395 if energy_column == "auto":
377 mu_column = input_values["merge_inputs"]["format"]["mu_column"] 396 energy_column = None
397 elif energy_column == "other":
398 energy_column_input = format_inputs["energy_column"]
399 energy_column = energy_column_input["energy_column_text"]
400
401 if "mu_column" not in format_inputs:
402 mu_column = None
403 else:
404 mu_column = format_inputs["mu_column"]["mu_column"]
405 if mu_column == "auto":
406 mu_column = None
407 elif mu_column == "other":
408 mu_column = format_inputs["mu_column"]["mu_column_text"]
378 409
379 reader = Reader( 410 reader = Reader(
380 energy_column=energy_column, 411 energy_column=energy_column,
381 mu_column=mu_column, 412 mu_column=mu_column,
382 data_format=data_format, 413 data_format=format_inputs["format"],
383 extract_group=extract_group, 414 extract_group=extract_group,
384 ) 415 )
385 keyed_data = reader.load_data( 416 keyed_data = reader.load_data(
386 dat_file=dat_file, 417 dat_file=dat_file,
387 merge_inputs=merge_inputs, 418 merge_inputs=merge_inputs,
394 425
395 do_rebin = input_values["processing"].pop("rebin") 426 do_rebin = input_values["processing"].pop("rebin")
396 427
397 pre_edge_items = input_values["processing"]["pre_edge"].items() 428 pre_edge_items = input_values["processing"]["pre_edge"].items()
398 pre_edge_settings = {k: v for k, v in pre_edge_items if v is not None} 429 pre_edge_settings = {k: v for k, v in pre_edge_items if v is not None}
399 do_pre_edge = pre_edge_settings.pop("pre_edge") == "true" 430 do_pre_edge = bool(pre_edge_settings.pop("pre_edge"))
431
432 ref_channel = None
433 if "ref_channel" in pre_edge_settings:
434 ref_channel = pre_edge_settings.pop("ref_channel")
400 435
401 xftf_items = input_values["processing"]["xftf"].items() 436 xftf_items = input_values["processing"]["xftf"].items()
402 xftf_settings = {k: v for k, v in xftf_items if v is not None} 437 xftf_settings = {k: v for k, v in xftf_items if v is not None}
403 do_xftf = xftf_settings.pop("xftf") == "true" 438 do_xftf = xftf_settings.pop("xftf") == "true"
404 439
411 do_calibrate=do_calibrate, 446 do_calibrate=do_calibrate,
412 calibrate_settings=calibrate_settings, 447 calibrate_settings=calibrate_settings,
413 do_rebin=do_rebin, 448 do_rebin=do_rebin,
414 do_pre_edge=do_pre_edge, 449 do_pre_edge=do_pre_edge,
415 pre_edge_settings=pre_edge_settings, 450 pre_edge_settings=pre_edge_settings,
451 ref_channel=ref_channel,
416 do_xftf=do_xftf, 452 do_xftf=do_xftf,
417 xftf_settings=xftf_settings, 453 xftf_settings=xftf_settings,
418 plot_graph=plot_graph, 454 plot_graph=plot_graph,
419 annotation=annotation, 455 annotation=annotation,
420 path_key=key, 456 path_key=key,