Changeset f80b416e in sasview for src/sas/sascalc
- Timestamp:
- Sep 20, 2017 12:21:41 PM (7 years ago)
- Branches:
- master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
- Children:
- fca1f50
- Parents:
- 2746eab (diff), ce0a245 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent. - Location:
- src/sas/sascalc
- Files:
-
- 9 edited
-
corfunc/corfunc_calculator.py (modified) (4 diffs)
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corfunc/transform_thread.py (modified) (5 diffs)
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dataloader/file_reader_base_class.py (modified) (5 diffs)
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dataloader/readers/cansas_reader.py (modified) (8 diffs)
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dataloader/readers/cansas_reader_HDF5.py (modified) (2 diffs)
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dataloader/readers/xml_reader.py (modified) (1 diff)
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invariant/invariant.py (modified) (4 diffs)
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calculator/sas_gen.py (modified) (1 diff)
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realspace/__init__.py (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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src/sas/sascalc/corfunc/corfunc_calculator.py
rff11b21 ra859f99 34 34 35 35 def __call__(self, x): 36 if self._lastx == [] or x.tolist() != self._lastx.tolist(): 36 # If input is a single number, evaluate the function at that number 37 # and return a single number 38 if type(x) == float or type(x) == int: 39 return self._smoothed_function(np.array([x]))[0] 40 # If input is a list, and is different to the last input, evaluate 41 # the function at each point. If the input is the same as last time 42 # the function was called, return the result that was calculated 43 # last time instead of explicity evaluating the function again. 44 elif self._lastx == [] or x.tolist() != self._lastx.tolist(): 37 45 self._lasty = self._smoothed_function(x) 38 46 self._lastx = x … … 121 129 extrapolation = Data1D(qs, iqs) 122 130 123 return params, extrapolation 131 return params, extrapolation, s2 124 132 125 133 def compute_transform(self, extrapolation, trans_type, background=None, … … 131 139 :param background: The background value (if not provided, previously 132 140 calculated value will be used) 141 :param extrap_fn: A callable function representing the extraoplated data 133 142 :param completefn: The function to call when the transform calculation 134 is complete `143 is complete 135 144 :param updatefn: The function to call to update the GUI with the status 136 145 of the transform calculation … … 144 153 if trans_type == 'fourier': 145 154 self._transform_thread = FourierThread(self._data, extrapolation, 146 background, completefn=completefn, updatefn=updatefn) 155 background, completefn=completefn, 156 updatefn=updatefn) 147 157 elif trans_type == 'hilbert': 148 158 self._transform_thread = HilbertThread(self._data, extrapolation, -
src/sas/sascalc/corfunc/transform_thread.py
rd03228e ra859f99 2 2 from sas.sascalc.dataloader.data_info import Data1D 3 3 from scipy.fftpack import dct 4 from scipy.integrate import trapz, cumtrapz 4 5 import numpy as np 5 6 from time import sleep … … 13 14 self.extrapolation = extrapolated_data 14 15 16 def check_if_cancelled(self): 17 if self.isquit(): 18 self.update("Fourier transform cancelled.") 19 self.complete(transforms=None) 20 return True 21 return False 22 15 23 def compute(self): 16 24 qs = self.extrapolation.x … … 19 27 background = self.background 20 28 29 xs = np.pi*np.arange(len(qs),dtype=np.float32)/(q[1]-q[0])/len(qs) 30 21 31 self.ready(delay=0.0) 22 self.update(msg=" Starting Fourier transform.")32 self.update(msg="Fourier transform in progress.") 23 33 self.ready(delay=0.0) 24 if self.isquit(): 25 34 35 if self.check_if_cancelled(): return 26 36 try: 27 gamma = dct((iqs-background)*qs**2) 28 gamma = gamma / gamma.max() 29 except: 37 # ----- 1D Correlation Function ----- 38 gamma1 = dct((iqs-background)*qs**2) 39 Q = gamma1.max() 40 gamma1 /= Q 41 42 if self.check_if_cancelled(): return 43 44 # ----- 3D Correlation Function ----- 45 # gamma3(R) = 1/R int_{0}^{R} gamma1(x) dx 46 # trapz uses the trapezium rule to calculate the integral 47 mask = xs <= 200.0 # Only calculate gamma3 up to x=200 (as this is all that's plotted) 48 # gamma3 = [trapz(gamma1[:n], xs[:n])/xs[n-1] for n in range(2, len(xs[mask]) + 1)]j 49 # gamma3.insert(0, 1.0) # Gamma_3(0) is defined as 1 50 n = len(xs[mask]) 51 gamma3 = cumtrapz(gamma1[:n], xs[:n])/xs[1:n] 52 gamma3 = np.hstack((1.0, gamma3)) # Gamma_3(0) is defined as 1 53 54 if self.check_if_cancelled(): return 55 56 # ----- Interface Distribution function ----- 57 idf = dct(-qs**4 * (iqs-background)) 58 59 if self.check_if_cancelled(): return 60 61 # Manually calculate IDF(0.0), since scipy DCT tends to give us a 62 # very large negative value. 63 # IDF(x) = int_0^inf q^4 * I(q) * cos(q*x) * dq 64 # => IDF(0) = int_0^inf q^4 * I(q) * dq 65 idf[0] = trapz(-qs**4 * (iqs-background), qs) 66 idf /= Q # Normalise using scattering invariant 67 68 except Exception as e: 69 import logging 70 logger = logging.getLogger(__name__) 71 logger.error(e) 72 30 73 self.update(msg="Fourier transform failed.") 31 self.complete(transform =None)74 self.complete(transforms=None) 32 75 return 33 76 if self.isquit(): … … 35 78 self.update(msg="Fourier transform completed.") 36 79 37 xs = np.pi*np.arange(len(qs),dtype=np.float32)/(q[1]-q[0])/len(qs) 38 transform = Data1D(xs, gamma) 80 transform1 = Data1D(xs, gamma1) 81 transform3 = Data1D(xs[xs <= 200], gamma3) 82 idf = Data1D(xs, idf) 39 83 40 self.complete(transform=transform) 84 transforms = (transform1, transform3, idf) 85 86 self.complete(transforms=transforms) 41 87 42 88 class HilbertThread(CalcThread): … … 64 110 self.update(msg="Hilbert transform completed.") 65 111 66 self.complete(transform =None)112 self.complete(transforms=None) -
src/sas/sascalc/dataloader/file_reader_base_class.py
ra78a02f rae69c690 115 115 data.y = np.asarray([data.y[i] for i in ind]).astype(np.float64) 116 116 if data.dx is not None: 117 if len(data.dx) == 0: 118 data.dx = None 119 continue 117 120 data.dx = np.asarray([data.dx[i] for i in ind]).astype(np.float64) 118 121 if data.dxl is not None: … … 121 124 data.dxw = np.asarray([data.dxw[i] for i in ind]).astype(np.float64) 122 125 if data.dy is not None: 126 if len(data.dy) == 0: 127 data.dy = None 128 continue 123 129 data.dy = np.asarray([data.dy[i] for i in ind]).astype(np.float64) 124 130 if data.lam is not None: … … 185 191 self.output = [] 186 192 187 def remove_empty_q_values(self, has_error_dx=False, has_error_dy=False): 193 def remove_empty_q_values(self, has_error_dx=False, has_error_dy=False, 194 has_error_dxl=False, has_error_dxw=False): 188 195 """ 189 196 Remove any point where Q == 0 … … 192 199 self.current_dataset.x = self.current_dataset.x[x != 0] 193 200 self.current_dataset.y = self.current_dataset.y[x != 0] 194 self.current_dataset.dy = self.current_dataset.dy[x != 0] if \ 195 has_error_dy else np.zeros(len(self.current_dataset.y)) 196 self.current_dataset.dx = self.current_dataset.dx[x != 0] if \ 197 has_error_dx else np.zeros(len(self.current_dataset.x)) 201 if has_error_dy: 202 self.current_dataset.dy = self.current_dataset.dy[x != 0] 203 if has_error_dx: 204 self.current_dataset.dx = self.current_dataset.dx[x != 0] 205 if has_error_dxl: 206 self.current_dataset.dxl = self.current_dataset.dxl[x != 0] 207 if has_error_dxw: 208 self.current_dataset.dxw = self.current_dataset.dxw[x != 0] 198 209 199 210 def reset_data_list(self, no_lines=0): … … 204 215 x = np.zeros(no_lines) 205 216 y = np.zeros(no_lines) 217 dx = np.zeros(no_lines) 206 218 dy = np.zeros(no_lines) 207 dx = np.zeros(no_lines)208 219 self.current_dataset = plottable_1D(x, y, dx, dy) 209 220 -
src/sas/sascalc/dataloader/readers/cansas_reader.py
ra78a02f rae69c690 130 130 self.current_datainfo.meta_data[PREPROCESS] = self.processing_instructions 131 131 self._parse_entry(entry) 132 has_error_dx = self.current_dataset.dx is not None 133 has_error_dy = self.current_dataset.dy is not None 134 self.remove_empty_q_values(has_error_dx=has_error_dx, 135 has_error_dy=has_error_dy) 136 self.send_to_output() # Combine datasets with DataInfo 137 self.current_datainfo = DataInfo() # Reset DataInfo 132 self.data_cleanup() 138 133 except FileContentsException as fc_exc: 139 134 # File doesn't meet schema - try loading with a less strict schema … … 154 149 self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file 155 150 invalid_xml = self.find_invalid_xml() 156 invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml 157 raise DataReaderException(invalid_xml) # Handled by base class 151 if invalid_xml != "": 152 invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml 153 raise DataReaderException(invalid_xml) # Handled by base class 158 154 except FileContentsException as fc_exc: 159 155 msg = "CanSAS Reader could not load the file {}".format(xml_file) … … 279 275 # I and Q points 280 276 elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D): 281 unit_list = unit.split("|") 282 if len(unit_list) > 1: 283 self.current_dataset.yaxis(unit_list[0].strip(), 284 unit_list[1].strip()) 285 else: 286 self.current_dataset.yaxis("Intensity", unit) 277 self.current_dataset.yaxis("Intensity", unit) 287 278 self.current_dataset.y = np.append(self.current_dataset.y, data_point) 288 279 elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D): 289 280 self.current_dataset.dy = np.append(self.current_dataset.dy, data_point) 290 281 elif tagname == 'Q': 291 unit_list = unit.split("|") 292 if len(unit_list) > 1: 293 self.current_dataset.xaxis(unit_list[0].strip(), 294 unit_list[1].strip()) 295 else: 296 self.current_dataset.xaxis("Q", unit) 282 self.current_dataset.xaxis("Q", unit) 297 283 self.current_dataset.x = np.append(self.current_dataset.x, data_point) 298 284 elif tagname == 'Qdev': 299 285 self.current_dataset.dx = np.append(self.current_dataset.dx, data_point) 300 286 elif tagname == 'dQw': 301 if self.current_dataset.dxw is None: 302 self.current_dataset.dxw = np.empty(0) 303 self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point) 287 self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point) 304 288 elif tagname == 'dQl': 305 if self.current_dataset.dxl is None:306 self.current_dataset.dxl = np.empty(0)307 289 self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point) 308 290 elif tagname == 'Qmean': … … 312 294 elif tagname == 'Sesans': 313 295 self.current_datainfo.isSesans = bool(data_point) 296 self.current_dataset.xaxis(attr.get('x_axis'), 297 attr.get('x_unit')) 298 self.current_dataset.yaxis(attr.get('y_axis'), 299 attr.get('y_unit')) 314 300 elif tagname == 'yacceptance': 315 301 self.current_datainfo.sample.yacceptance = (data_point, unit) … … 512 498 for error in self.errors: 513 499 self.current_datainfo.errors.add(error) 514 self.errors.clear() 515 self.send_to_output() 500 self.data_cleanup() 501 self.sort_one_d_data() 502 self.sort_two_d_data() 503 self.reset_data_list() 516 504 empty = None 517 505 return self.output[0], empty 506 507 def data_cleanup(self): 508 """ 509 Clean up the data sets and refresh everything 510 :return: None 511 """ 512 has_error_dx = self.current_dataset.dx is not None 513 has_error_dxl = self.current_dataset.dxl is not None 514 has_error_dxw = self.current_dataset.dxw is not None 515 has_error_dy = self.current_dataset.dy is not None 516 self.remove_empty_q_values(has_error_dx=has_error_dx, 517 has_error_dxl=has_error_dxl, 518 has_error_dxw=has_error_dxw, 519 has_error_dy=has_error_dy) 520 self.send_to_output() # Combine datasets with DataInfo 521 self.current_datainfo = DataInfo() # Reset DataInfo 518 522 519 523 def _is_call_local(self): … … 642 646 value_unit = local_unit 643 647 except KeyError: 644 err_msg = "CanSAS reader: unexpected " 645 err_msg += "\"{0}\" unit [{1}]; " 646 err_msg = err_msg.format(tagname, local_unit) 647 err_msg += "expecting [{0}]".format(default_unit) 648 # Do not throw an error for loading Sesans data in cansas xml 649 # This is a temporary fix. 650 if local_unit != "A" and local_unit != 'pol': 651 err_msg = "CanSAS reader: unexpected " 652 err_msg += "\"{0}\" unit [{1}]; " 653 err_msg = err_msg.format(tagname, local_unit) 654 err_msg += "expecting [{0}]".format(default_unit) 648 655 value_unit = local_unit 649 656 except: … … 675 682 di_exists = True 676 683 if dqw_exists and not dql_exists: 677 array_size = self.current_dataset.dxw.size - 1 678 self.current_dataset.dxl = np.append(self.current_dataset.dxl, 679 np.zeros([array_size])) 684 array_size = self.current_dataset.dxw.size 685 self.current_dataset.dxl = np.zeros(array_size) 680 686 elif dql_exists and not dqw_exists: 681 array_size = self.current_dataset.dxl.size - 1 682 self.current_dataset.dxw = np.append(self.current_dataset.dxw, 683 np.zeros([array_size])) 687 array_size = self.current_dataset.dxl.size 688 self.current_dataset.dxw = np.zeros(array_size) 684 689 elif not dql_exists and not dqw_exists and not dq_exists: 685 array_size = self.current_dataset.x.size - 1690 array_size = self.current_dataset.x.size 686 691 self.current_dataset.dx = np.append(self.current_dataset.dx, 687 692 np.zeros([array_size])) 688 693 if not di_exists: 689 array_size = self.current_dataset.y.size - 1694 array_size = self.current_dataset.y.size 690 695 self.current_dataset.dy = np.append(self.current_dataset.dy, 691 696 np.zeros([array_size])) … … 857 862 node.append(point) 858 863 self.write_node(point, "Q", datainfo.x[i], 859 {'unit': datainfo. _xaxis + " | " + datainfo._xunit})864 {'unit': datainfo.x_unit}) 860 865 if len(datainfo.y) >= i: 861 866 self.write_node(point, "I", datainfo.y[i], 862 {'unit': datainfo. _yaxis + " | " + datainfo._yunit})867 {'unit': datainfo.y_unit}) 863 868 if datainfo.dy is not None and len(datainfo.dy) > i: 864 869 self.write_node(point, "Idev", datainfo.dy[i], 865 {'unit': datainfo. _yaxis + " | " + datainfo._yunit})870 {'unit': datainfo.y_unit}) 866 871 if datainfo.dx is not None and len(datainfo.dx) > i: 867 872 self.write_node(point, "Qdev", datainfo.dx[i], 868 {'unit': datainfo. _xaxis + " | " + datainfo._xunit})873 {'unit': datainfo.x_unit}) 869 874 if datainfo.dxw is not None and len(datainfo.dxw) > i: 870 875 self.write_node(point, "dQw", datainfo.dxw[i], 871 {'unit': datainfo. _xaxis + " | " + datainfo._xunit})876 {'unit': datainfo.x_unit}) 872 877 if datainfo.dxl is not None and len(datainfo.dxl) > i: 873 878 self.write_node(point, "dQl", datainfo.dxl[i], 874 {'unit': datainfo. _xaxis + " | " + datainfo._xunit})879 {'unit': datainfo.x_unit}) 875 880 if datainfo.isSesans: 876 sesans = self.create_element("Sesans") 881 sesans_attrib = {'x_axis': datainfo._xaxis, 882 'y_axis': datainfo._yaxis, 883 'x_unit': datainfo.x_unit, 884 'y_unit': datainfo.y_unit} 885 sesans = self.create_element("Sesans", attrib=sesans_attrib) 877 886 sesans.text = str(datainfo.isSesans) 878 node.append(sesans)879 self.write_node( node, "yacceptance", datainfo.sample.yacceptance[0],887 entry_node.append(sesans) 888 self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0], 880 889 {'unit': datainfo.sample.yacceptance[1]}) 881 self.write_node( node, "zacceptance", datainfo.sample.zacceptance[0],890 self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0], 882 891 {'unit': datainfo.sample.zacceptance[1]}) 883 892 -
src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py
rdcb91cf rcd57c7d4 140 140 141 141 if isinstance(value, h5py.Group): 142 # Set parent class before recursion 142 143 self.parent_class = class_name 143 144 parent_list.append(key) … … 150 151 # Recursion step to access data within the group 151 152 self.read_children(value, parent_list) 153 # Reset parent class when returning from recursive method 154 self.parent_class = class_name 152 155 self.add_intermediate() 153 156 parent_list.remove(key) -
src/sas/sascalc/dataloader/readers/xml_reader.py
rfafe52a rcd57c7d4 134 134 first_error = schema.assertValid(self.xmldoc) 135 135 except etree.DocumentInvalid as err: 136 # Suppress errors for <'any'> elements 137 if "##other" in str(err): 138 return first_error 136 139 first_error = str(err) 137 140 return first_error -
src/sas/sascalc/invariant/invariant.py
r7432acb rb1f20d1 610 610 # Data boundaries for fitting 611 611 qmin = self._data.x[0] 612 qmax = self._data.x[ self._low_extrapolation_npts - 1]612 qmax = self._data.x[int(self._low_extrapolation_npts - 1)] 613 613 614 614 # Extrapolate the low-Q data … … 649 649 # Data boundaries for fitting 650 650 x_len = len(self._data.x) - 1 651 qmin = self._data.x[ x_len - (self._high_extrapolation_npts - 1)]652 qmax = self._data.x[ x_len]651 qmin = self._data.x[int(x_len - (self._high_extrapolation_npts - 1))] 652 qmax = self._data.x[int(x_len)] 653 653 654 654 # fit the data with a model to get the appropriate parameters … … 688 688 if npts_in is None: 689 689 npts_in = self._low_extrapolation_npts 690 q_end = self._data.x[max(0, npts_in - 1)]690 q_end = self._data.x[max(0, int(npts_in - 1))] 691 691 692 692 if q_start >= q_end: … … 714 714 # Get extrapolation range 715 715 if npts_in is None: 716 npts_in = self._high_extrapolation_npts716 npts_in = int(self._high_extrapolation_npts) 717 717 _npts = len(self._data.x) 718 q_start = self._data.x[min(_npts, _npts - npts_in)]718 q_start = self._data.x[min(_npts, int(_npts - npts_in))] 719 719 720 720 if q_start >= q_end: -
src/sas/sascalc/calculator/sas_gen.py
ra1b8fee rf2ea95a 913 913 def set_sldms(self, sld_mx, sld_my, sld_mz): 914 914 r""" 915 Sets (\|m\|, m_theta, m_phi)916 """ 915 Sets mx, my, mz and abs(m). 916 """ # Note: escaping 917 917 if sld_mx.__class__.__name__ == 'float': 918 918 self.sld_mx = np.ones(len(self.pos_x)) * sld_mx -
src/sas/sascalc/realspace/__init__.py
r959eb01 rf2ea95a 1 1 """ 2 2 Real-Space Modeling for SAS 3 """ 3 """ 4 4 ## \mainpage Real-Space Modeling for SAS 5 5 # 6 6 # \section intro_sec Introduction 7 # This module provides SAS scattering intensity simulation 7 # This module provides SAS scattering intensity simulation 8 8 # based on real-space modeling. 9 9 # 10 # Documentation can be found here: 10 # Documentation can be found here: 11 11 # http://danse.us/trac/sas/wiki/RealSpaceModeling 12 12 # … … 37 37 # 38 38 # \section overview_sec Package Overview 39 # 39 # 40 40 # \subsection class Class Diagram: 41 41 # \image html real-space-class-diagram.png 42 42 # 43 43 # \subsection behav Behavior Enumeration: 44 # \image html enum. gif44 # \image html enum.png 45 45 # 46 46 # \subsection Tutorial … … 78 78 # \section help_sec Contact Info 79 79 # Code and Documentation by Jing Zhou as part of the DANSE project. 80
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