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comparison msnc_tools.py @ 3:f9c52762c32c draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
author rv43
date Tue, 05 Apr 2022 18:23:54 +0000
parents e4778148df6b
children baf9f5eef128
comparison
equal deleted inserted replaced
2:b8977c98800b 3:f9c52762c32c
295 illegal_value('title', title, 'clearFig') 295 illegal_value('title', title, 'clearFig')
296 return 296 return
297 plt.close(fig=re.sub(r"\s+", '_', title)) 297 plt.close(fig=re.sub(r"\s+", '_', title))
298 298
299 def quickImshow(a, title=None, path=None, name=None, save_fig=False, save_only=False, 299 def quickImshow(a, title=None, path=None, name=None, save_fig=False, save_only=False,
300 clear=True, **kwargs): 300 clear=True, extent=None, show_grid=False, grid_color='w', grid_linewidth=1, **kwargs):
301 if title is not None and not isinstance(title, str): 301 if title is not None and not isinstance(title, str):
302 illegal_value('title', title, 'quickImshow') 302 illegal_value('title', title, 'quickImshow')
303 return 303 return
304 if path is not None and not isinstance(path, str): 304 if path is not None and not isinstance(path, str):
305 illegal_value('path', path, 'quickImshow') 305 illegal_value('path', path, 'quickImshow')
325 else: 325 else:
326 if path is None: 326 if path is None:
327 path = name 327 path = name
328 else: 328 else:
329 path = f'{path}/{name}' 329 path = f'{path}/{name}'
330 if extent is None:
331 extent = (0, a.shape[1], a.shape[0], 0)
330 if clear: 332 if clear:
331 plt.close(fig=title) 333 plt.close(fig=title)
332 if save_only: 334 if save_only:
333 plt.figure(title) 335 plt.figure(title)
334 plt.imshow(a, **kwargs) 336 plt.imshow(a, extent=extent, **kwargs)
337 if show_grid:
338 ax = plt.gca()
339 ax.grid(color=grid_color, linewidth=grid_linewidth)
335 plt.savefig(path) 340 plt.savefig(path)
336 plt.close(fig=title) 341 plt.close(fig=title)
337 #plt.imsave(f'{title}.png', a, **kwargs) 342 #plt.imsave(f'{title}.png', a, **kwargs)
338 else: 343 else:
339 plt.ion() 344 plt.ion()
340 plt.figure(title) 345 plt.figure(title)
341 plt.imshow(a, **kwargs) 346 plt.imshow(a, extent=extent, **kwargs)
347 if show_grid:
348 ax = plt.gca()
349 ax.grid(color=grid_color, linewidth=grid_linewidth)
342 if save_fig: 350 if save_fig:
343 plt.savefig(path) 351 plt.savefig(path)
344 plt.pause(1) 352 plt.pause(1)
345 353
346 def quickPlot(*args, title=None, path=None, name=None, save_fig=False, save_only=False, 354 def quickPlot(*args, title=None, path=None, name=None, save_fig=False, save_only=False,
347 clear=True, **kwargs): 355 clear=True, show_grid=False, **kwargs):
348 if title is not None and not isinstance(title, str): 356 if title is not None and not isinstance(title, str):
349 illegal_value('title', title, 'quickPlot') 357 illegal_value('title', title, 'quickPlot')
350 return 358 return
351 if path is not None and not isinstance(path, str): 359 if path is not None and not isinstance(path, str):
352 illegal_value('path', path, 'quickPlot') 360 illegal_value('path', path, 'quickPlot')
381 if depth_tuple(args) > 1: 389 if depth_tuple(args) > 1:
382 for y in args: 390 for y in args:
383 plt.plot(*y, **kwargs) 391 plt.plot(*y, **kwargs)
384 else: 392 else:
385 plt.plot(*args, **kwargs) 393 plt.plot(*args, **kwargs)
394 if show_grid:
395 ax = plt.gca()
396 ax.grid(color='k')#, linewidth=1)
386 plt.savefig(path) 397 plt.savefig(path)
387 plt.close(fig=title) 398 plt.close(fig=title)
388 else: 399 else:
389 plt.ion() 400 plt.ion()
390 plt.figure(title) 401 plt.figure(title)
391 if depth_tuple(args) > 1: 402 if depth_tuple(args) > 1:
392 for y in args: 403 for y in args:
393 plt.plot(*y, **kwargs) 404 plt.plot(*y, **kwargs)
394 else: 405 else:
395 plt.plot(*args, **kwargs) 406 plt.plot(*args, **kwargs)
407 if show_grid:
408 ax = plt.gca()
409 ax.grid(color='k')#, linewidth=1)
396 if save_fig: 410 if save_fig:
397 plt.savefig(path) 411 plt.savefig(path)
398 plt.pause(1) 412 plt.pause(1)
399 413
400 def selectArrayBounds(a, x_low=None, x_upp=None, num_x_min=None, 414 def selectArrayBounds(a, x_low=None, x_upp=None, num_x_min=None,
534 else: 548 else:
535 if not is_int(upp, low+num_min, a.shape[axis]): 549 if not is_int(upp, low+num_min, a.shape[axis]):
536 illegal_value('upp', upp, 'selectImageBounds') 550 illegal_value('upp', upp, 'selectImageBounds')
537 return None 551 return None
538 bounds = [low, upp] 552 bounds = [low, upp]
539 a_tmp = a 553 a_tmp = np.copy(a)
554 a_tmp_max = a.max()
540 if axis: 555 if axis:
541 a_tmp[:,bounds[0]] = a.max() 556 a_tmp[:,bounds[0]] = a_tmp_max
542 a_tmp[:,bounds[1]] = a.max() 557 a_tmp[:,bounds[1]-1] = a_tmp_max
543 else: 558 else:
544 a_tmp[bounds[0],:] = a.max() 559 a_tmp[bounds[0],:] = a_tmp_max
545 a_tmp[bounds[1],:] = a.max() 560 a_tmp[bounds[1]-1,:] = a_tmp_max
546 print(f'lower bound = {low} (inclusive)\nupper bound = {upp} (exclusive)') 561 print(f'lower bound = {low} (inclusive)\nupper bound = {upp} (exclusive)')
547 quickImshow(a_tmp, title=title) 562 quickImshow(a_tmp, title=title)
563 del a_tmp
548 if pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True) == 'no': 564 if pyip.inputYesNo('Accept these bounds ([y]/n)?: ', blank=True) == 'no':
549 bounds = selectImageBounds(a, axis, low=low_save, upp=upp_save, num_min=num_min_save, 565 bounds = selectImageBounds(a, axis, low=low_save, upp=upp_save, num_min=num_min_save,
550 title=title) 566 title=title)
551 return bounds 567 return bounds
552 568