1 | """ |
---|
2 | Module that contains classes to hold information read from |
---|
3 | reduced data files. |
---|
4 | |
---|
5 | A good description of the data members can be found in |
---|
6 | the CanSAS 1D XML data format: |
---|
7 | |
---|
8 | http://www.smallangles.net/wgwiki/index.php/cansas1d_documentation |
---|
9 | """ |
---|
10 | |
---|
11 | """ |
---|
12 | This software was developed by the University of Tennessee as part of the |
---|
13 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
---|
14 | project funded by the US National Science Foundation. |
---|
15 | |
---|
16 | If you use DANSE applications to do scientific research that leads to |
---|
17 | publication, we ask that you acknowledge the use of the software with the |
---|
18 | following sentence: |
---|
19 | |
---|
20 | "This work benefited from DANSE software developed under NSF award DMR-0520547." |
---|
21 | |
---|
22 | copyright 2008, University of Tennessee |
---|
23 | """ |
---|
24 | |
---|
25 | #TODO: Keep track of data manipulation in the 'process' data structure. |
---|
26 | #TODO: This module should be independent of plottables. We should write |
---|
27 | # an adapter class for plottables when needed. |
---|
28 | |
---|
29 | #from sans.guitools.plottables import Data1D as plottable_1D |
---|
30 | from data_util.uncertainty import Uncertainty |
---|
31 | import numpy |
---|
32 | import math |
---|
33 | |
---|
34 | class plottable_1D: |
---|
35 | """ |
---|
36 | Data1D is a place holder for 1D plottables. |
---|
37 | """ |
---|
38 | # The presence of these should be mutually exclusive with the presence of Qdev (dx) |
---|
39 | x = None |
---|
40 | y = None |
---|
41 | dx = None |
---|
42 | dy = None |
---|
43 | ## Slit smearing length |
---|
44 | dxl = None |
---|
45 | ## Slit smearing width |
---|
46 | dxw = None |
---|
47 | |
---|
48 | # Units |
---|
49 | _xaxis = '' |
---|
50 | _xunit = '' |
---|
51 | _yaxis = '' |
---|
52 | _yunit = '' |
---|
53 | |
---|
54 | def __init__(self,x,y,dx=None,dy=None,dxl=None,dxw=None): |
---|
55 | self.x = x |
---|
56 | self.y = y |
---|
57 | self.dx = dx |
---|
58 | self.dy = dy |
---|
59 | self.dxl = dxl |
---|
60 | self.dxw = dxw |
---|
61 | |
---|
62 | def xaxis(self, label, unit): |
---|
63 | self._xaxis = label |
---|
64 | self._xunit = unit |
---|
65 | |
---|
66 | def yaxis(self, label, unit): |
---|
67 | self._yaxis = label |
---|
68 | self._yunit = unit |
---|
69 | |
---|
70 | class plottable_2D: |
---|
71 | """ |
---|
72 | Data2D is a place holder for 2D plottables. |
---|
73 | """ |
---|
74 | xmin = None |
---|
75 | xmax = None |
---|
76 | ymin = None |
---|
77 | ymax = None |
---|
78 | data = None |
---|
79 | err_data = None |
---|
80 | |
---|
81 | # Units |
---|
82 | _xaxis = '' |
---|
83 | _xunit = '' |
---|
84 | _yaxis = '' |
---|
85 | _yunit = '' |
---|
86 | _zaxis = '' |
---|
87 | _zunit = '' |
---|
88 | |
---|
89 | def __init__(self, data=None, err_data=None): |
---|
90 | self.data = numpy.asarray(data) |
---|
91 | self.err_data = numpy.asarray(err_data) |
---|
92 | |
---|
93 | def xaxis(self, label, unit): |
---|
94 | self._xaxis = label |
---|
95 | self._xunit = unit |
---|
96 | |
---|
97 | def yaxis(self, label, unit): |
---|
98 | self._yaxis = label |
---|
99 | self._yunit = unit |
---|
100 | |
---|
101 | def zaxis(self, label, unit): |
---|
102 | self._zaxis = label |
---|
103 | self._zunit = unit |
---|
104 | |
---|
105 | |
---|
106 | class Vector: |
---|
107 | """ |
---|
108 | Vector class to hold multi-dimensional objects |
---|
109 | """ |
---|
110 | ## x component |
---|
111 | x = None |
---|
112 | ## y component |
---|
113 | y = None |
---|
114 | ## z component |
---|
115 | z = None |
---|
116 | |
---|
117 | def __init__(self, x=None, y=None, z=None): |
---|
118 | """ |
---|
119 | Initialization. Components that are not |
---|
120 | set a set to None by default. |
---|
121 | |
---|
122 | @param x: x component |
---|
123 | @param y: y component |
---|
124 | @param z: z component |
---|
125 | """ |
---|
126 | self.x = x |
---|
127 | self.y = y |
---|
128 | self.z = z |
---|
129 | |
---|
130 | def __str__(self): |
---|
131 | return "x = %s\ty = %s\tz = %s" % (str(self.x), str(self.y), str(self.z)) |
---|
132 | |
---|
133 | |
---|
134 | class Detector: |
---|
135 | """ |
---|
136 | Class to hold detector information |
---|
137 | """ |
---|
138 | ## Name of the instrument [string] |
---|
139 | name = None |
---|
140 | ## Sample to detector distance [float] [mm] |
---|
141 | distance = None |
---|
142 | distance_unit = 'mm' |
---|
143 | ## Offset of this detector position in X, Y, (and Z if necessary) [Vector] [mm] |
---|
144 | offset = None |
---|
145 | offset_unit = 'm' |
---|
146 | ## Orientation (rotation) of this detector in roll, pitch, and yaw [Vector] [degrees] |
---|
147 | orientation = None |
---|
148 | orientation_unit = 'degree' |
---|
149 | ## Center of the beam on the detector in X and Y (and Z if necessary) [Vector] [mm] |
---|
150 | beam_center = None |
---|
151 | beam_center_unit = 'mm' |
---|
152 | ## Pixel size in X, Y, (and Z if necessary) [Vector] [mm] |
---|
153 | pixel_size = None |
---|
154 | pixel_size_unit = 'mm' |
---|
155 | ## Slit length of the instrument for this detector.[float] [mm] |
---|
156 | slit_length = None |
---|
157 | slit_length_unit = 'mm' |
---|
158 | |
---|
159 | def __init__(self): |
---|
160 | """ |
---|
161 | Initialize class attribute that are objects... |
---|
162 | """ |
---|
163 | self.offset = Vector() |
---|
164 | self.orientation = Vector() |
---|
165 | self.beam_center = Vector() |
---|
166 | self.pixel_size = Vector() |
---|
167 | |
---|
168 | |
---|
169 | def __str__(self): |
---|
170 | _str = "Detector:\n" |
---|
171 | _str += " Name: %s\n" % self.name |
---|
172 | _str += " Distance: %s [%s]\n" % \ |
---|
173 | (str(self.distance), str(self.distance_unit)) |
---|
174 | _str += " Offset: %s [%s]\n" % \ |
---|
175 | (str(self.offset), str(self.offset_unit)) |
---|
176 | _str += " Orientation: %s [%s]\n" % \ |
---|
177 | (str(self.orientation), str(self.orientation_unit)) |
---|
178 | _str += " Beam center: %s [%s]\n" % \ |
---|
179 | (str(self.beam_center), str(self.beam_center_unit)) |
---|
180 | _str += " Pixel size: %s [%s]\n" % \ |
---|
181 | (str(self.pixel_size), str(self.pixel_size_unit)) |
---|
182 | _str += " Slit length: %s [%s]\n" % \ |
---|
183 | (str(self.slit_length), str(self.slit_length_unit)) |
---|
184 | return _str |
---|
185 | |
---|
186 | class Aperture: |
---|
187 | ## Name |
---|
188 | name = None |
---|
189 | ## Type |
---|
190 | type = None |
---|
191 | ## Size name |
---|
192 | size_name = None |
---|
193 | ## Aperture size [Vector] |
---|
194 | size = None |
---|
195 | size_unit = 'mm' |
---|
196 | ## Aperture distance [float] |
---|
197 | distance = None |
---|
198 | distance_unit = 'mm' |
---|
199 | |
---|
200 | def __init__(self): |
---|
201 | self.size = Vector() |
---|
202 | |
---|
203 | class Collimation: |
---|
204 | """ |
---|
205 | Class to hold collimation information |
---|
206 | """ |
---|
207 | ## Name |
---|
208 | name = None |
---|
209 | ## Length [float] [mm] |
---|
210 | length = None |
---|
211 | length_unit = 'mm' |
---|
212 | ## Aperture |
---|
213 | aperture = None |
---|
214 | |
---|
215 | def __init__(self): |
---|
216 | self.aperture = [] |
---|
217 | |
---|
218 | def __str__(self): |
---|
219 | _str = "Collimation:\n" |
---|
220 | _str += " Length: %s [%s]\n" % \ |
---|
221 | (str(self.length), str(self.length_unit)) |
---|
222 | for item in self.aperture: |
---|
223 | _str += " Aperture size:%s [%s]\n" % \ |
---|
224 | (str(item.size), str(item.size_unit)) |
---|
225 | _str += " Aperture_dist:%s [%s]\n" % \ |
---|
226 | (str(item.distance), str(item.distance_unit)) |
---|
227 | return _str |
---|
228 | |
---|
229 | class Source: |
---|
230 | """ |
---|
231 | Class to hold source information |
---|
232 | """ |
---|
233 | ## Name |
---|
234 | name = None |
---|
235 | ## Radiation type [string] |
---|
236 | radiation = None |
---|
237 | ## Beam size name |
---|
238 | beam_size_name = None |
---|
239 | ## Beam size [Vector] [mm] |
---|
240 | beam_size = None |
---|
241 | beam_size_unit = 'mm' |
---|
242 | ## Beam shape [string] |
---|
243 | beam_shape = None |
---|
244 | ## Wavelength [float] [Angstrom] |
---|
245 | wavelength = None |
---|
246 | wavelength_unit = 'A' |
---|
247 | ## Minimum wavelength [float] [Angstrom] |
---|
248 | wavelength_min = None |
---|
249 | wavelength_min_unit = 'nm' |
---|
250 | ## Maximum wavelength [float] [Angstrom] |
---|
251 | wavelength_max = None |
---|
252 | wavelength_max_unit = 'nm' |
---|
253 | ## Wavelength spread [float] [Angstrom] |
---|
254 | wavelength_spread = None |
---|
255 | wavelength_spread_unit = 'percent' |
---|
256 | |
---|
257 | def __init__(self): |
---|
258 | self.beam_size = Vector() |
---|
259 | |
---|
260 | |
---|
261 | def __str__(self): |
---|
262 | _str = "Source:\n" |
---|
263 | _str += " Radiation: %s\n" % str(self.radiation) |
---|
264 | _str += " Shape: %s\n" % str(self.beam_shape) |
---|
265 | _str += " Wavelength: %s [%s]\n" % \ |
---|
266 | (str(self.wavelength), str(self.wavelength_unit)) |
---|
267 | _str += " Waveln_min: %s [%s]\n" % \ |
---|
268 | (str(self.wavelength_min), str(self.wavelength_min_unit)) |
---|
269 | _str += " Waveln_max: %s [%s]\n" % \ |
---|
270 | (str(self.wavelength_max), str(self.wavelength_max_unit)) |
---|
271 | _str += " Waveln_spread:%s [%s]\n" % \ |
---|
272 | (str(self.wavelength_spread), str(self.wavelength_spread_unit)) |
---|
273 | _str += " Beam_size: %s [%s]\n" % \ |
---|
274 | (str(self.beam_size), str(self.beam_size_unit)) |
---|
275 | return _str |
---|
276 | |
---|
277 | |
---|
278 | """ |
---|
279 | Definitions of radiation types |
---|
280 | """ |
---|
281 | NEUTRON = 'neutron' |
---|
282 | XRAY = 'x-ray' |
---|
283 | MUON = 'muon' |
---|
284 | ELECTRON = 'electron' |
---|
285 | |
---|
286 | class Sample: |
---|
287 | """ |
---|
288 | Class to hold the sample description |
---|
289 | """ |
---|
290 | ## Short name for sample |
---|
291 | name = '' |
---|
292 | ## ID |
---|
293 | ID = '' |
---|
294 | ## Thickness [float] [mm] |
---|
295 | thickness = None |
---|
296 | thickness_unit = 'mm' |
---|
297 | ## Transmission [float] [fraction] |
---|
298 | transmission = None |
---|
299 | ## Temperature [float] [C] |
---|
300 | temperature = None |
---|
301 | temperature_unit = 'C' |
---|
302 | ## Position [Vector] [mm] |
---|
303 | position = None |
---|
304 | position_unit = 'mm' |
---|
305 | ## Orientation [Vector] [degrees] |
---|
306 | orientation = None |
---|
307 | orientation_unit = 'degree' |
---|
308 | ## Details |
---|
309 | details = None |
---|
310 | |
---|
311 | def __init__(self): |
---|
312 | self.position = Vector() |
---|
313 | self.orientation = Vector() |
---|
314 | self.details = [] |
---|
315 | |
---|
316 | def __str__(self): |
---|
317 | _str = "Sample:\n" |
---|
318 | _str += " ID: %s\n" % str(self.ID) |
---|
319 | _str += " Transmission: %s\n" % str(self.transmission) |
---|
320 | _str += " Thickness: %s [%s]\n" % \ |
---|
321 | (str(self.thickness), str(self.thickness_unit)) |
---|
322 | _str += " Temperature: %s [%s]\n" % \ |
---|
323 | (str(self.temperature), str(self.temperature_unit)) |
---|
324 | _str += " Position: %s [%s]\n" % \ |
---|
325 | (str(self.position), str(self.position_unit)) |
---|
326 | _str += " Orientation: %s [%s]\n" % \ |
---|
327 | (str(self.orientation), str(self.orientation_unit)) |
---|
328 | |
---|
329 | _str += " Details:\n" |
---|
330 | for item in self.details: |
---|
331 | _str += " %s\n" % item |
---|
332 | |
---|
333 | return _str |
---|
334 | |
---|
335 | class Process: |
---|
336 | """ |
---|
337 | Class that holds information about the processes |
---|
338 | performed on the data. |
---|
339 | """ |
---|
340 | name = '' |
---|
341 | date = '' |
---|
342 | description= '' |
---|
343 | term = None |
---|
344 | notes = None |
---|
345 | |
---|
346 | def __init__(self): |
---|
347 | self.term = [] |
---|
348 | self.notes = [] |
---|
349 | |
---|
350 | def __str__(self): |
---|
351 | _str = "Process:\n" |
---|
352 | _str += " Name: %s\n" % self.name |
---|
353 | _str += " Date: %s\n" % self.date |
---|
354 | _str += " Description: %s\n" % self.description |
---|
355 | for item in self.term: |
---|
356 | _str += " Term: %s\n" % item |
---|
357 | for item in self.notes: |
---|
358 | _str += " Note: %s\n" % item |
---|
359 | return _str |
---|
360 | |
---|
361 | |
---|
362 | class DataInfo: |
---|
363 | """ |
---|
364 | Class to hold the data read from a file. |
---|
365 | It includes four blocks of data for the |
---|
366 | instrument description, the sample description, |
---|
367 | the data itself and any other meta data. |
---|
368 | """ |
---|
369 | ## Title |
---|
370 | title = '' |
---|
371 | ## Run number |
---|
372 | run = None |
---|
373 | ## Run name |
---|
374 | run_name = None |
---|
375 | ## File name |
---|
376 | filename = '' |
---|
377 | ## Notes |
---|
378 | notes = None |
---|
379 | ## Processes (Action on the data) |
---|
380 | process = None |
---|
381 | ## Instrument name |
---|
382 | instrument = '' |
---|
383 | ## Detector information |
---|
384 | detector = None |
---|
385 | ## Sample information |
---|
386 | sample = None |
---|
387 | ## Source information |
---|
388 | source = None |
---|
389 | ## Collimation information |
---|
390 | collimation = None |
---|
391 | ## Additional meta-data |
---|
392 | meta_data = None |
---|
393 | ## Loading errors |
---|
394 | errors = None |
---|
395 | |
---|
396 | def __init__(self): |
---|
397 | """ |
---|
398 | Initialization |
---|
399 | """ |
---|
400 | ## Title |
---|
401 | self.title = '' |
---|
402 | ## Run number |
---|
403 | self.run = [] |
---|
404 | self.run_name = {} |
---|
405 | ## File name |
---|
406 | self.filename = '' |
---|
407 | ## Notes |
---|
408 | self.notes = [] |
---|
409 | ## Processes (Action on the data) |
---|
410 | self.process = [] |
---|
411 | ## Instrument name |
---|
412 | self.instrument = '' |
---|
413 | ## Detector information |
---|
414 | self.detector = [] |
---|
415 | ## Sample information |
---|
416 | self.sample = Sample() |
---|
417 | ## Source information |
---|
418 | self.source = Source() |
---|
419 | ## Collimation information |
---|
420 | self.collimation = [] |
---|
421 | ## Additional meta-data |
---|
422 | self.meta_data = {} |
---|
423 | ## Loading errors |
---|
424 | self.errors = [] |
---|
425 | |
---|
426 | def __str__(self): |
---|
427 | """ |
---|
428 | Nice printout |
---|
429 | """ |
---|
430 | _str = "File: %s\n" % self.filename |
---|
431 | _str += "Title: %s\n" % self.title |
---|
432 | _str += "Run: %s\n" % str(self.run) |
---|
433 | _str += "Instrument: %s\n" % str(self.instrument) |
---|
434 | _str += "%s\n" % str(self.sample) |
---|
435 | _str += "%s\n" % str(self.source) |
---|
436 | for item in self.detector: |
---|
437 | _str += "%s\n" % str(item) |
---|
438 | for item in self.collimation: |
---|
439 | _str += "%s\n" % str(item) |
---|
440 | for item in self.process: |
---|
441 | _str += "%s\n" % str(item) |
---|
442 | for item in self.notes: |
---|
443 | _str += "%s\n" % str(item) |
---|
444 | |
---|
445 | return _str |
---|
446 | |
---|
447 | # Private method to perform operation. Not implemented for DataInfo, |
---|
448 | # but should be implemented for each data class inherited from DataInfo |
---|
449 | # that holds actual data (ex.: Data1D) |
---|
450 | def _perform_operation(self, other, operation): return NotImplemented |
---|
451 | |
---|
452 | def __add__(self, other): |
---|
453 | """ |
---|
454 | Add two data sets |
---|
455 | |
---|
456 | @param other: data set to add to the current one |
---|
457 | @return: new data set |
---|
458 | @raise ValueError: raised when two data sets are incompatible |
---|
459 | """ |
---|
460 | def operation(a, b): return a+b |
---|
461 | return self._perform_operation(other, operation) |
---|
462 | |
---|
463 | def __radd__(self, other): |
---|
464 | """ |
---|
465 | Add two data sets |
---|
466 | |
---|
467 | @param other: data set to add to the current one |
---|
468 | @return: new data set |
---|
469 | @raise ValueError: raised when two data sets are incompatible |
---|
470 | """ |
---|
471 | def operation(a, b): return b+a |
---|
472 | return self._perform_operation(other, operation) |
---|
473 | |
---|
474 | def __sub__(self, other): |
---|
475 | """ |
---|
476 | Subtract two data sets |
---|
477 | |
---|
478 | @param other: data set to subtract from the current one |
---|
479 | @return: new data set |
---|
480 | @raise ValueError: raised when two data sets are incompatible |
---|
481 | """ |
---|
482 | def operation(a, b): return a-b |
---|
483 | return self._perform_operation(other, operation) |
---|
484 | |
---|
485 | def __rsub__(self, other): |
---|
486 | """ |
---|
487 | Subtract two data sets |
---|
488 | |
---|
489 | @param other: data set to subtract from the current one |
---|
490 | @return: new data set |
---|
491 | @raise ValueError: raised when two data sets are incompatible |
---|
492 | """ |
---|
493 | def operation(a, b): return b-a |
---|
494 | return self._perform_operation(other, operation) |
---|
495 | |
---|
496 | def __mul__(self, other): |
---|
497 | """ |
---|
498 | Multiply two data sets |
---|
499 | |
---|
500 | @param other: data set to subtract from the current one |
---|
501 | @return: new data set |
---|
502 | @raise ValueError: raised when two data sets are incompatible |
---|
503 | """ |
---|
504 | def operation(a, b): return a*b |
---|
505 | return self._perform_operation(other, operation) |
---|
506 | |
---|
507 | def __rmul__(self, other): |
---|
508 | """ |
---|
509 | Multiply two data sets |
---|
510 | |
---|
511 | @param other: data set to subtract from the current one |
---|
512 | @return: new data set |
---|
513 | @raise ValueError: raised when two data sets are incompatible |
---|
514 | """ |
---|
515 | def operation(a, b): return b*a |
---|
516 | return self._perform_operation(other, operation) |
---|
517 | |
---|
518 | def __div__(self, other): |
---|
519 | """ |
---|
520 | Divided a data set by another |
---|
521 | |
---|
522 | @param other: data set that the current one is divided by |
---|
523 | @return: new data set |
---|
524 | @raise ValueError: raised when two data sets are incompatible |
---|
525 | """ |
---|
526 | def operation(a, b): return a/b |
---|
527 | return self._perform_operation(other, operation) |
---|
528 | |
---|
529 | def __rdiv__(self, other): |
---|
530 | """ |
---|
531 | Divided a data set by another |
---|
532 | |
---|
533 | @param other: data set that the current one is divided by |
---|
534 | @return: new data set |
---|
535 | @raise ValueError: raised when two data sets are incompatible |
---|
536 | """ |
---|
537 | def operation(a, b): return b/a |
---|
538 | return self._perform_operation(other, operation) |
---|
539 | |
---|
540 | class Data1D(plottable_1D, DataInfo): |
---|
541 | """ |
---|
542 | 1D data class |
---|
543 | """ |
---|
544 | x_unit = '1/A' |
---|
545 | y_unit = '1/cm' |
---|
546 | |
---|
547 | def __init__(self, x, y, dx=None, dy=None): |
---|
548 | DataInfo.__init__(self) |
---|
549 | plottable_1D.__init__(self, x, y, dx, dy) |
---|
550 | |
---|
551 | |
---|
552 | def __str__(self): |
---|
553 | """ |
---|
554 | Nice printout |
---|
555 | """ |
---|
556 | _str = "%s\n" % DataInfo.__str__(self) |
---|
557 | |
---|
558 | _str += "Data:\n" |
---|
559 | _str += " Type: %s\n" % self.__class__.__name__ |
---|
560 | _str += " X-axis: %s\t[%s]\n" % (self._xaxis, self._xunit) |
---|
561 | _str += " Y-axis: %s\t[%s]\n" % (self._yaxis, self._yunit) |
---|
562 | _str += " Length: %g\n" % len(self.x) |
---|
563 | |
---|
564 | return _str |
---|
565 | |
---|
566 | def is_slit_smeared(self): |
---|
567 | """ |
---|
568 | Check whether the data has slit smearing information |
---|
569 | |
---|
570 | @return: True is slit smearing info is present, False otherwise |
---|
571 | """ |
---|
572 | def _check(v): |
---|
573 | if (v.__class__==list or v.__class__==numpy.ndarray) \ |
---|
574 | and len(v)>0 and min(v)>0: |
---|
575 | return True |
---|
576 | |
---|
577 | return False |
---|
578 | |
---|
579 | return _check(self.dxl) or _check(self.dxw) |
---|
580 | |
---|
581 | def clone_without_data(self, length=0, clone=None): |
---|
582 | """ |
---|
583 | Clone the current object, without copying the data (which |
---|
584 | will be filled out by a subsequent operation). |
---|
585 | The data arrays will be initialized to zero. |
---|
586 | |
---|
587 | @param length: length of the data array to be initialized |
---|
588 | @param clone: if provided, the data will be copied to clone |
---|
589 | """ |
---|
590 | from copy import deepcopy |
---|
591 | |
---|
592 | if clone is None or not issubclass(clone.__class__, Data1D): |
---|
593 | x = numpy.zeros(length) |
---|
594 | dx = numpy.zeros(length) |
---|
595 | y = numpy.zeros(length) |
---|
596 | dy = numpy.zeros(length) |
---|
597 | clone = Data1D(x, y, dx=dx, dy=dy) |
---|
598 | |
---|
599 | clone.title = self.title |
---|
600 | clone.run = self.run |
---|
601 | clone.filename = self.filename |
---|
602 | clone.notes = deepcopy(self.notes) |
---|
603 | clone.process = deepcopy(self.process) |
---|
604 | clone.detector = deepcopy(self.detector) |
---|
605 | clone.sample = deepcopy(self.sample) |
---|
606 | clone.source = deepcopy(self.source) |
---|
607 | clone.collimation = deepcopy(self.collimation) |
---|
608 | clone.meta_data = deepcopy(self.meta_data) |
---|
609 | clone.errors = deepcopy(self.errors) |
---|
610 | |
---|
611 | return clone |
---|
612 | |
---|
613 | def _validity_check(self, other): |
---|
614 | """ |
---|
615 | Checks that the data lengths are compatible. |
---|
616 | Checks that the x vectors are compatible. |
---|
617 | Returns errors vectors equal to original |
---|
618 | errors vectors if they were present or vectors |
---|
619 | of zeros when none was found. |
---|
620 | |
---|
621 | @param other: other data set for operation |
---|
622 | @return: dy for self, dy for other [numpy arrays] |
---|
623 | @raise ValueError: when lengths are not compatible |
---|
624 | """ |
---|
625 | dy_other = None |
---|
626 | if isinstance(other, Data1D): |
---|
627 | # Check that data lengths are the same |
---|
628 | if len(self.x) != len(other.x) or \ |
---|
629 | len(self.y) != len(other.y): |
---|
630 | raise ValueError, "Unable to perform operation: data length are not equal" |
---|
631 | |
---|
632 | # Here we could also extrapolate between data points |
---|
633 | for i in range(len(self.x)): |
---|
634 | if self.x[i] != other.x[i]: |
---|
635 | raise ValueError, "Incompatible data sets: x-values do not match" |
---|
636 | |
---|
637 | # Check that the other data set has errors, otherwise |
---|
638 | # create zero vector |
---|
639 | dy_other = other.dy |
---|
640 | if other.dy==None or (len(other.dy) != len(other.y)): |
---|
641 | dy_other = numpy.zeros(len(other.y)) |
---|
642 | |
---|
643 | # Check that we have errors, otherwise create zero vector |
---|
644 | dy = self.dy |
---|
645 | if self.dy==None or (len(self.dy) != len(self.y)): |
---|
646 | dy = numpy.zeros(len(self.y)) |
---|
647 | |
---|
648 | return dy, dy_other |
---|
649 | |
---|
650 | def _perform_operation(self, other, operation): |
---|
651 | """ |
---|
652 | """ |
---|
653 | # First, check the data compatibility |
---|
654 | dy, dy_other = self._validity_check(other) |
---|
655 | result = self.clone_without_data(len(self.x)) |
---|
656 | |
---|
657 | for i in range(len(self.x)): |
---|
658 | result.x[i] = self.x[i] |
---|
659 | if self.dx is not None and len(self.x)==len(self.dx): |
---|
660 | result.dx[i] = self.dx[i] |
---|
661 | |
---|
662 | a = Uncertainty(self.y[i], dy[i]**2) |
---|
663 | if isinstance(other, Data1D): |
---|
664 | b = Uncertainty(other.y[i], dy_other[i]**2) |
---|
665 | else: |
---|
666 | b = other |
---|
667 | |
---|
668 | output = operation(a, b) |
---|
669 | result.y[i] = output.x |
---|
670 | result.dy[i] = math.sqrt(math.fabs(output.variance)) |
---|
671 | return result |
---|
672 | |
---|
673 | class Data2D(plottable_2D, DataInfo): |
---|
674 | """ |
---|
675 | 2D data class |
---|
676 | """ |
---|
677 | ## Units for Q-values |
---|
678 | Q_unit = '1/A' |
---|
679 | |
---|
680 | ## Units for I(Q) values |
---|
681 | I_unit = '1/cm' |
---|
682 | |
---|
683 | ## Vector of Q-values at the center of each bin in x |
---|
684 | x_bins = None |
---|
685 | |
---|
686 | ## Vector of Q-values at the center of each bin in y |
---|
687 | y_bins = None |
---|
688 | |
---|
689 | |
---|
690 | def __init__(self, data=None, err_data=None): |
---|
691 | self.y_bins = [] |
---|
692 | self.x_bins = [] |
---|
693 | DataInfo.__init__(self) |
---|
694 | plottable_2D.__init__(self, data, err_data) |
---|
695 | if len(self.detector)>0: |
---|
696 | raise RuntimeError, "Data2D: Detector bank already filled at init" |
---|
697 | |
---|
698 | def __str__(self): |
---|
699 | _str = "%s\n" % DataInfo.__str__(self) |
---|
700 | |
---|
701 | _str += "Data:\n" |
---|
702 | _str += " Type: %s\n" % self.__class__.__name__ |
---|
703 | _str += " X- & Y-axis: %s\t[%s]\n" % (self._yaxis, self._yunit) |
---|
704 | _str += " Z-axis: %s\t[%s]\n" % (self._zaxis, self._zunit) |
---|
705 | leny = 0 |
---|
706 | if len(self.data)>0: |
---|
707 | leny = len(self.data[0]) |
---|
708 | _str += " Length: %g x %g\n" % (len(self.data), leny) |
---|
709 | |
---|
710 | return _str |
---|
711 | |
---|
712 | def clone_without_data(self, length=0, clone=None): |
---|
713 | """ |
---|
714 | Clone the current object, without copying the data (which |
---|
715 | will be filled out by a subsequent operation). |
---|
716 | The data arrays will be initialized to zero. |
---|
717 | |
---|
718 | @param length: length of the data array to be initialized |
---|
719 | @param clone: if provided, the data will be copied to clone |
---|
720 | """ |
---|
721 | from copy import deepcopy |
---|
722 | |
---|
723 | if clone is None or not issubclass(clone.__class__, Data2D): |
---|
724 | data = numpy.zeros(length) |
---|
725 | err_data = numpy.zeros(length) |
---|
726 | clone = Data2D(data, err_data) |
---|
727 | |
---|
728 | clone.title = self.title |
---|
729 | clone.run = self.run |
---|
730 | clone.filename = self.filename |
---|
731 | clone.notes = deepcopy(self.notes) |
---|
732 | clone.process = deepcopy(self.process) |
---|
733 | clone.detector = deepcopy(self.detector) |
---|
734 | clone.sample = deepcopy(self.sample) |
---|
735 | clone.source = deepcopy(self.source) |
---|
736 | clone.collimation = deepcopy(self.collimation) |
---|
737 | clone.meta_data = deepcopy(self.meta_data) |
---|
738 | clone.errors = deepcopy(self.errors) |
---|
739 | |
---|
740 | return clone |
---|
741 | |
---|
742 | |
---|
743 | def _validity_check(self, other): |
---|
744 | """ |
---|
745 | Checks that the data lengths are compatible. |
---|
746 | Checks that the x vectors are compatible. |
---|
747 | Returns errors vectors equal to original |
---|
748 | errors vectors if they were present or vectors |
---|
749 | of zeros when none was found. |
---|
750 | |
---|
751 | @param other: other data set for operation |
---|
752 | @return: dy for self, dy for other [numpy arrays] |
---|
753 | @raise ValueError: when lengths are not compatible |
---|
754 | """ |
---|
755 | err_other = None |
---|
756 | if isinstance(other, Data2D): |
---|
757 | # Check that data lengths are the same |
---|
758 | if numpy.size(self.data) != numpy.size(other.data): |
---|
759 | raise ValueError, "Unable to perform operation: data length are not equal" |
---|
760 | |
---|
761 | # Check that the scales match |
---|
762 | #TODO: matching scales? |
---|
763 | |
---|
764 | # Check that the other data set has errors, otherwise |
---|
765 | # create zero vector |
---|
766 | #TODO: test this |
---|
767 | err_other = other.err_data |
---|
768 | if other.err_data==None or (numpy.size(other.err_data) != numpy.size(other.data)): |
---|
769 | err_other = numpy.zeros([numpy.size(other.data,0), numpy.size(other.data,1)]) |
---|
770 | |
---|
771 | # Check that we have errors, otherwise create zero vector |
---|
772 | err = self.err_data |
---|
773 | if self.err_data==None or (numpy.size(self.err_data) != numpy.size(self.data)): |
---|
774 | err = numpy.zeros([numpy.size(self.data,0), numpy.size(self.data,1)]) |
---|
775 | |
---|
776 | return err, err_other |
---|
777 | |
---|
778 | |
---|
779 | def _perform_operation(self, other, operation): |
---|
780 | """ |
---|
781 | Perform 2D operations between data sets |
---|
782 | |
---|
783 | @param other: other data set |
---|
784 | @param operation: function defining the operation |
---|
785 | """ |
---|
786 | # First, check the data compatibility |
---|
787 | dy, dy_other = self._validity_check(other) |
---|
788 | |
---|
789 | result = self.clone_without_data([numpy.size(self.data,0), numpy.size(self.data,1)]) |
---|
790 | |
---|
791 | for i in range(numpy.size(self.data,0)): |
---|
792 | for j in range(numpy.size(self.data,1)): |
---|
793 | result.data[i][j] = self.data[i][j] |
---|
794 | if self.err_data is not None and numpy.size(self.data)==numpy.size(self.err_data): |
---|
795 | result.err_data[i][j] = self.err_data[i][j] |
---|
796 | |
---|
797 | a = Uncertainty(self.data[i][j], dy[i][j]**2) |
---|
798 | if isinstance(other, Data2D): |
---|
799 | b = Uncertainty(other.data[i][j], dy_other[i][j]**2) |
---|
800 | else: |
---|
801 | b = other |
---|
802 | |
---|
803 | output = operation(a, b) |
---|
804 | result.data[i][j] = output.x |
---|
805 | result.err_data[i][j] = math.sqrt(math.fabs(output.variance)) |
---|
806 | return result |
---|
807 | |
---|
808 | |
---|
809 | |
---|