1 | import time |
---|
2 | import sys |
---|
3 | import os |
---|
4 | import logging |
---|
5 | import sas.sascalc.dataloader |
---|
6 | from lxml import etree |
---|
7 | from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader |
---|
8 | from sas.sascalc.dataloader.readers.cansas_reader import get_content |
---|
9 | from sas.sasgui.guiframe.utils import format_number |
---|
10 | from sas.sasgui.guiframe.gui_style import GUIFRAME_ID |
---|
11 | from sas.sasgui.guiframe.dataFitting import Data1D |
---|
12 | from sas.sascalc.dataloader.data_info import Data1D as LoaderData1D |
---|
13 | from sas.sascalc.dataloader.loader import Loader |
---|
14 | |
---|
15 | logger = logging.getLogger(__name__) |
---|
16 | |
---|
17 | CORNODE_NAME = 'corfunc' |
---|
18 | CANSAS_NS = 'cansas1d/1.0' |
---|
19 | |
---|
20 | # The default state |
---|
21 | DEFAULT_STATE = { |
---|
22 | 'qmin_tcl': None, |
---|
23 | 'qmax1_tcl': None, |
---|
24 | 'qmax2_tcl': None, |
---|
25 | 'background_tcl': None |
---|
26 | } |
---|
27 | |
---|
28 | # List of output parameters, used by __str__ |
---|
29 | output_list = [ |
---|
30 | ['max', "Long Period (A): "], |
---|
31 | ['Lc', "Average Hard Block Thickness (A): "], |
---|
32 | ['dtr', "Average Interface Thickness (A): "], |
---|
33 | ['d0', "Average Core Thickness: "], |
---|
34 | ['A', "PolyDispersity: "], |
---|
35 | ['fill', "Filling Fraction: "] |
---|
36 | ] |
---|
37 | |
---|
38 | class CorfuncState(object): |
---|
39 | """ |
---|
40 | Stores information about the state of CorfuncPanel |
---|
41 | """ |
---|
42 | |
---|
43 | def __init__(self): |
---|
44 | # Inputs |
---|
45 | self.file = None |
---|
46 | self.data = None |
---|
47 | self.qmin = None |
---|
48 | self.qmax = [0, 0] |
---|
49 | self.background = None |
---|
50 | self.outputs = {} |
---|
51 | self.is_extrapolated = False |
---|
52 | self.transform_type = 'fourier' |
---|
53 | self.is_transformed = False |
---|
54 | |
---|
55 | self.saved_state = DEFAULT_STATE |
---|
56 | self.timestamp = time.time() |
---|
57 | |
---|
58 | # Raw Data |
---|
59 | self.q = None |
---|
60 | self.iq = None |
---|
61 | # TODO: Add extrapolated data and transformed data (when implemented) |
---|
62 | |
---|
63 | def __str__(self): |
---|
64 | """ |
---|
65 | Pretty print the state |
---|
66 | |
---|
67 | :return: A string representing the state |
---|
68 | """ |
---|
69 | state = "File: {}\n".format(self.file) |
---|
70 | state += "Timestamp: {}\n".format(self.timestamp) |
---|
71 | state += "Qmin: {}\n".format(str(self.qmin)) |
---|
72 | state += "Qmax: {}\n".format(str(self.qmax)) |
---|
73 | state += "Background: {}\n".format(str(self.background)) |
---|
74 | |
---|
75 | if self.outputs != {} and self.outputs is not None: |
---|
76 | state += "\nOutputs:\n" |
---|
77 | for key, value in self.outputs.iteritems(): |
---|
78 | name = output_list[key][1] |
---|
79 | state += "{}: {}\n".format(name, str(value)) |
---|
80 | |
---|
81 | return state |
---|
82 | |
---|
83 | def set_saved_state(self, name, value): |
---|
84 | """ |
---|
85 | Set a value in the current state. |
---|
86 | |
---|
87 | :param name: The name of the parameter to set |
---|
88 | :param value: The value to set the parameter to |
---|
89 | """ |
---|
90 | self.saved_state[name] = value |
---|
91 | if name == 'qmin_tcl': |
---|
92 | self.qmin = value |
---|
93 | elif name == 'qmax1_tcl': |
---|
94 | self.qmax[0] = value |
---|
95 | elif name == 'qmax2_tcl': |
---|
96 | self.qmax[1] = value |
---|
97 | elif name == 'background_tcl': |
---|
98 | self.background = value |
---|
99 | |
---|
100 | def toXML(self, filename='corfunc_state.crf', doc=None, entry_node=None): |
---|
101 | """ |
---|
102 | Writes the state of the CorfuncPanel panel to file, as XML. |
---|
103 | |
---|
104 | Compatible with standalone writing, or appending to an |
---|
105 | already existing XML document. In that case, the XML document |
---|
106 | is required. An optional entry node in the XML document |
---|
107 | may also be given. |
---|
108 | |
---|
109 | :param file: file to write to |
---|
110 | :param doc: XML document object [optional] |
---|
111 | :param entry_node: XML node within the XML document at which |
---|
112 | we will append the data [optional] |
---|
113 | |
---|
114 | :return: None if no doc is provided, modified XML document if doc!=None |
---|
115 | """ |
---|
116 | from xml.dom.minidom import getDOMImplementation |
---|
117 | |
---|
118 | top_element = None |
---|
119 | new_doc = None |
---|
120 | if doc is None: |
---|
121 | # Create a new XML document |
---|
122 | impl = getDOMImplementation() |
---|
123 | doc_type = impl.createDocumentType(CORNODE_NAME, "1.0", "1.0") |
---|
124 | new_doc = impl.createDocument(None, CORNODE_NAME, doc_type) |
---|
125 | top_element = new_doc.documentElement |
---|
126 | else: |
---|
127 | # Create a new element in the document provided |
---|
128 | top_element = doc.createElement(CORNODE_NAME) |
---|
129 | if entry_node is None: |
---|
130 | doc.documentElement.appendChild(top_element) |
---|
131 | else: |
---|
132 | entry_node.appendChild(top_element) |
---|
133 | new_doc = doc |
---|
134 | |
---|
135 | # Version |
---|
136 | attr = new_doc.createAttribute("version") |
---|
137 | attr.nodeValue = '1.0' |
---|
138 | top_element.setAttributeNode(attr) |
---|
139 | |
---|
140 | # Filename |
---|
141 | element = new_doc.createElement("filename") |
---|
142 | if self.file is not None and self.file != '': |
---|
143 | element.appendChild(new_doc.createTextNode(str(self.file))) |
---|
144 | else: |
---|
145 | element.appendChild(new_doc.createTextNode(str(filename))) |
---|
146 | top_element.appendChild(element) |
---|
147 | |
---|
148 | # Timestamp |
---|
149 | element = new_doc.createElement("timestamp") |
---|
150 | # Pretty printed format |
---|
151 | element.appendChild(new_doc.createTextNode(time.ctime(self.timestamp))) |
---|
152 | attr = new_doc.createAttribute("epoch") |
---|
153 | # Epoch value (used in self.fromXML) |
---|
154 | attr.nodeValue = str(self.timestamp) |
---|
155 | element.setAttributeNode(attr) |
---|
156 | top_element.appendChild(element) |
---|
157 | |
---|
158 | # Current state |
---|
159 | state = new_doc.createElement("state") |
---|
160 | top_element.appendChild(state) |
---|
161 | for name, value in self.saved_state.iteritems(): |
---|
162 | element = new_doc.createElement(name) |
---|
163 | element.appendChild(new_doc.createTextNode(str(value))) |
---|
164 | state.appendChild(element) |
---|
165 | |
---|
166 | # Whether or not the extrapolate & transform buttons have been clicked |
---|
167 | element = new_doc.createElement("is_extrapolated") |
---|
168 | top_element.appendChild(element) |
---|
169 | element.appendChild(new_doc.createTextNode(str(int(self.is_extrapolated)))) |
---|
170 | |
---|
171 | element = new_doc.createElement("is_transformed") |
---|
172 | top_element.appendChild(element) |
---|
173 | element.appendChild(new_doc.createTextNode(str(int(self.is_transformed)))) |
---|
174 | |
---|
175 | if self.is_transformed: |
---|
176 | element = new_doc.createElement("transform_type") |
---|
177 | top_element.appendChild(element) |
---|
178 | element.appendChild(new_doc.createTextNode(self.transform_type)) |
---|
179 | |
---|
180 | # Output parameters |
---|
181 | if self.outputs != {} and self.outputs is not None: |
---|
182 | output = new_doc.createElement("output") |
---|
183 | top_element.appendChild(output) |
---|
184 | for key, value in self.outputs.iteritems(): |
---|
185 | element = new_doc.createElement(key) |
---|
186 | element.appendChild(new_doc.createTextNode(str(value))) |
---|
187 | output.appendChild(element) |
---|
188 | |
---|
189 | # Save the file or return the original document with the state |
---|
190 | # data appended |
---|
191 | if doc is None: |
---|
192 | fd = open(filename, 'w') |
---|
193 | fd.write(new_doc.toprettyxml()) |
---|
194 | fd.close() |
---|
195 | return None |
---|
196 | else: |
---|
197 | return new_doc |
---|
198 | |
---|
199 | |
---|
200 | def fromXML(self, node): |
---|
201 | """ |
---|
202 | Load corfunc states from a file |
---|
203 | |
---|
204 | :param node: node of an XML document to read from (optional) |
---|
205 | """ |
---|
206 | if node.get('version') and node.get('version') == '1.0': |
---|
207 | # Parse filename |
---|
208 | entry = get_content('ns:filename', node) |
---|
209 | if entry is not None: |
---|
210 | self.file = entry.text.strip() |
---|
211 | |
---|
212 | # Parse timestamp |
---|
213 | entry = get_content('ns:timestamp', node) |
---|
214 | if entry is not None and entry.get('epoch'): |
---|
215 | try: |
---|
216 | self.timestamp = (entry.get('epoch')) |
---|
217 | except: |
---|
218 | msg = ("CorfuncState.fromXML: Could not read timestamp", |
---|
219 | "\n{}").format(sys.exc_value) |
---|
220 | logger.error(msg) |
---|
221 | |
---|
222 | # Parse current state |
---|
223 | entry = get_content('ns:state', node) |
---|
224 | if entry is not None: |
---|
225 | for item in DEFAULT_STATE.iterkeys(): |
---|
226 | input_field = get_content("ns:{}".format(item), entry) |
---|
227 | if input_field is not None: |
---|
228 | try: |
---|
229 | value = float(input_field.text.strip()) |
---|
230 | except: |
---|
231 | value = None |
---|
232 | self.set_saved_state(name=item, value=value) |
---|
233 | |
---|
234 | # Parse is_extrapolated and is_transformed |
---|
235 | entry = get_content('ns:is_extrapolated', node) |
---|
236 | if entry is not None: |
---|
237 | self.is_extrapolated = bool(int(entry.text.strip())) |
---|
238 | entry = get_content('ns:is_transformed', node) |
---|
239 | if entry is not None: |
---|
240 | self.is_transformed = bool(int(entry.text.strip())) |
---|
241 | entry = get_content('ns:transform_type', node) |
---|
242 | self.transform_type = entry.text.strip() |
---|
243 | |
---|
244 | # Parse outputs |
---|
245 | entry = get_content('ns:output', node) |
---|
246 | if entry is not None: |
---|
247 | for item in output_list: |
---|
248 | parameter = get_content("ns:{}".format(item[0]), entry) |
---|
249 | if parameter is not None: |
---|
250 | self.outputs[item[0]] = float(parameter.text.strip()) |
---|
251 | |
---|
252 | |
---|
253 | |
---|
254 | class Reader(CansasReader): |
---|
255 | """ |
---|
256 | Reads a CanSAS file containing the state of a CorfuncPanel |
---|
257 | """ |
---|
258 | |
---|
259 | type_name = "Corfunc" |
---|
260 | |
---|
261 | type = ["Corfunc file (*.crf)|*.crf", |
---|
262 | "SASView file (*.svs)|*.svs"] |
---|
263 | |
---|
264 | ext = ['.crf', '.CRF', '.svs', '.SVS'] |
---|
265 | |
---|
266 | def __init__(self, callback): |
---|
267 | self.callback = callback |
---|
268 | self.state = None |
---|
269 | |
---|
270 | def read(self, path): |
---|
271 | """ |
---|
272 | Load data and corfunc information frmo a CanSAS file. |
---|
273 | |
---|
274 | :param path: The file path to read from |
---|
275 | :return: Data1D object, a list of Data1D objects, or None |
---|
276 | :raise IOError: When the file can't be found |
---|
277 | :raise IOError: When the file is an invalid file type |
---|
278 | :raise ValueError: When the length of the data vectors are inconsistent |
---|
279 | """ |
---|
280 | output = [] |
---|
281 | if os.path.isfile(path): |
---|
282 | # Load file |
---|
283 | basename = os.path.basename(path) |
---|
284 | root, ext = os.path.splitext(basename) |
---|
285 | if not ext.lower() in self.ext: |
---|
286 | raise IOError, "{} is not a supported file type".format(ext) |
---|
287 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
288 | root = tree.getroot() |
---|
289 | entry_list = root.xpath('/ns:SASroot/ns:SASentry', |
---|
290 | namespaces={'ns': CANSAS_NS}) |
---|
291 | for entry in entry_list: |
---|
292 | sas_entry, _ = self._parse_entry(entry) |
---|
293 | corstate = self._parse_state(entry) |
---|
294 | |
---|
295 | if corstate is not None: |
---|
296 | sas_entry.meta_data['corstate'] = corstate |
---|
297 | sas_entry.filename = corstate.file |
---|
298 | output.append(sas_entry) |
---|
299 | else: |
---|
300 | # File not found |
---|
301 | msg = "{} is not a valid file path or doesn't exist".format(path) |
---|
302 | raise IOError, msg |
---|
303 | |
---|
304 | if len(output) == 0: |
---|
305 | return None |
---|
306 | elif len(output) == 1: |
---|
307 | self.callback(output[0].meta_data['corstate'], datainfo=output[0]) |
---|
308 | return output[0] |
---|
309 | else: |
---|
310 | return output |
---|
311 | |
---|
312 | def write(self, filename, datainfo=None, state=None): |
---|
313 | """ |
---|
314 | Write the content of a Data1D as a CanSAS file. |
---|
315 | |
---|
316 | : param filename: Name of the file to write |
---|
317 | : param datainfo: Data1D object |
---|
318 | : param state: CorfuncState object |
---|
319 | """ |
---|
320 | # Prepare datainfo |
---|
321 | if datainfo is None: |
---|
322 | datainfo = Data1D(x=[], y=[]) |
---|
323 | elif not (isinstance(datainfo, Data1D) or isinstance(datainfo, LoaderData1D)): |
---|
324 | msg = ("The CanSAS writer expects a Data1D instance. {} was " |
---|
325 | "provided").format(datainfo.__class__.__name__) |
---|
326 | raise RuntimeError, msg |
---|
327 | if datainfo.title is None or datainfo.title == '': |
---|
328 | datainfo.title = datainfo.name |
---|
329 | if datainfo.run_name is None or datainfo.run_name == '': |
---|
330 | datainfo.run = [str(datainfo.name)] |
---|
331 | datainfo.run_name[0] = datainfo.name |
---|
332 | |
---|
333 | # Create the XMl doc |
---|
334 | doc, sasentry = self._to_xml_doc(datainfo) |
---|
335 | if state is not None: |
---|
336 | doc = state.toXML(doc=doc, entry_node=sasentry) |
---|
337 | |
---|
338 | # Write the XML doc to a file |
---|
339 | fd = open(filename, 'w') |
---|
340 | fd.write(doc.toprettyxml()) |
---|
341 | fd.close() |
---|
342 | |
---|
343 | def get_state(self): |
---|
344 | return self.state |
---|
345 | |
---|
346 | |
---|
347 | def _parse_state(self, entry): |
---|
348 | """ |
---|
349 | Read state data from an XML node |
---|
350 | |
---|
351 | :param entry: The XML node to read from |
---|
352 | :return: CorfuncState object |
---|
353 | """ |
---|
354 | state = None |
---|
355 | try: |
---|
356 | nodes = entry.xpath('ns:{}'.format(CORNODE_NAME), |
---|
357 | namespaces={'ns': CANSAS_NS}) |
---|
358 | if nodes != []: |
---|
359 | state = CorfuncState() |
---|
360 | state.fromXML(nodes[0]) |
---|
361 | except: |
---|
362 | msg = "XML document does not contain CorfuncState information\n{}" |
---|
363 | msg.format(sys.exc_value) |
---|
364 | logger.info(msg) |
---|
365 | return state |
---|