Changeset 9687d58 in sasview for src/sas/sascalc/dataloader/readers

Timestamp:

Apr 10, 2017 4:01:46 AM (7 years ago)

Author:

Piotr Rozyczko <rozyczko@…>

Branches:

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

Children:

6c8fb2c

Parents:

9208346 (diff), c6f3aec (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.

Message:

Merge branch 'master' into ESS_GUI

Location:

src/sas/sascalc/dataloader/readers

Files:

• anton_paar_saxs_reader.py (modified) (4 diffs)
• ascii_reader.py (modified) (1 diff)
• cansas_reader.py (modified) (1 diff)
• cansas_reader_HDF5.py (modified) (5 diffs)
• xml_reader.py (modified) (1 diff)

src/sas/sascalc/dataloader/readers/anton_paar_saxs_reader.py

@@ -45 +45 @@
     output = None
 
-    def __init__(self):
+    def reset_state(self):
         self.current_dataset = Data1D(np.empty(0), np.empty(0),
                                             np.empty(0), np.empty(0))
@@ -72 +72 @@
 
         ## Reinitialize the class when loading a new data file to reset all class variables
-        self.__init__()
+        self.reset_state()
         ## Check that the file exists
         if os.path.isfile(filename):
@@ -84 +84 @@
                 self.raw_data = buff.splitlines()
                 self.read_data()
-                xml_intermediate = self.raw_data[self.upper:]
-                xml = ''.join(xml_intermediate)
-                self.set_xml_file(xml)
         return self.output
 
@@ -100 +97 @@
         self.lower = 5
         self.upper = self.lower + self.data_points
-        self.detector.distance = float(line4[1])
+        self.source.radiation = 'x-ray'
+        normal = float(line4[3])
         self.current_dataset.source.radiation = "x-ray"
         self.current_dataset.source.name = "Anton Paar SAXSess Instrument"
         self.current_dataset.source.wavelength = float(line4[4])
-        normal = line4[3]
+        xvals = []
+        yvals = []
+        dyvals = []
         for i in range(self.lower, self.upper):
+            index = i - self.lower
             data = self.raw_data[i].split()
-            x_val = [float(data[0])]
-            y_val = [float(data[1])]
-            dy_val = [float(data[2])]
-            self.current_dataset.x = np.append(self.current_dataset.x, x_val)
-            self.current_dataset.y = np.append(self.current_dataset.y, y_val)
-            self.current_dataset.dy = np.append(self.current_dataset.dy, dy_val)
-        self.current_dataset.xaxis("Q (%s)" % (q_unit), q_unit)
-        self.current_dataset.yaxis("Intensity (%s)" % (i_unit), i_unit)
-        self.current_dataset.detector.append(self.detector)
+            xvals.insert(index, normal * float(data[0]))
+            yvals.insert(index, normal * float(data[1]))
+            dyvals.insert(index, normal * float(data[2]))
+        self.current_dataset.x = np.append(self.current_dataset.x, xvals)
+        self.current_dataset.y = np.append(self.current_dataset.y, yvals)
+        self.current_dataset.dy = np.append(self.current_dataset.dy, dyvals)
+        if self.data_points != self.current_dataset.x.size:
+            self.errors.add("Not all data was loaded properly.")
+        if self.current_dataset.dx.size != self.current_dataset.x.size:
+            dxvals = np.zeros(self.current_dataset.x.size)
+            self.current_dataset.dx = dxvals
+        if self.current_dataset.x.size != self.current_dataset.y.size:
+            self.errors.add("The x and y data sets are not the same size.")
+        if self.current_dataset.y.size != self.current_dataset.dy.size:
+            self.errors.add("The y and dy datasets are not the same size.")
+        self.current_dataset.errors = self.errors
+        self.current_dataset.xaxis("Q", q_unit)
+        self.current_dataset.yaxis("Intensity", i_unit)
+        xml_intermediate = self.raw_data[self.upper:]
+        xml = ''.join(xml_intermediate)
+        self.set_xml_string(xml)
+        dom = self.xmlroot.xpath('/fileinfo')
+        self._parse_child(dom)
         self.output.append(self.current_dataset)
+
+    def _parse_child(self, dom, parent=''):
+        """
+        Recursive method for stepping through the embedded XML
+        :param dom: XML node with or without children
+        """
+        for node in dom:
+            tagname = node.tag
+            value = node.text
+            attr = node.attrib
+            key = attr.get("key", '')
+            if len(node.getchildren()) > 1:
+                self._parse_child(node, key)
+                if key == "SampleDetector":
+                    self.current_dataset.detector.append(self.detector)
+                    self.detector = Detector()
+            else:
+                if key == "value":
+                    if parent == "Wavelength":
+                        self.current_dataset.source.wavelength = value
+                    elif parent == "SampleDetector":
+                        self.detector.distance = value
+                    elif parent == "Temperature":
+                        self.current_dataset.sample.temperature = value
+                    elif parent == "CounterSlitLength":
+                        self.detector.slit_length = value
+                elif key == "unit":
+                    value = value.replace("_", "")
+                    if parent == "Wavelength":
+                        self.current_dataset.source.wavelength_unit = value
+                    elif parent == "SampleDetector":
+                        self.detector.distance_unit = value
+                    elif parent == "X":
+                        self.current_dataset.xaxis(self.current_dataset._xaxis, value)
+                    elif parent == "Y":
+                        self.current_dataset.yaxis(self.current_dataset._yaxis, value)
+                    elif parent == "Temperature":
+                        self.current_dataset.sample.temperature_unit = value
+                    elif parent == "CounterSlitLength":
+                        self.detector.slit_length_unit = value
+                elif key == "quantity":
+                    if parent == "X":
+                        self.current_dataset.xaxis(value, self.current_dataset._xunit)
+                    elif parent == "Y":
+                        self.current_dataset.yaxis(value, self.current_dataset._yunit)

src/sas/sascalc/dataloader/readers/ascii_reader.py

@@ -172 +172 @@
                 input_f.close()
                 if not is_data:
-                    return None
+                    msg = "ascii_reader: x has no data"
+                    raise RuntimeError, msg
                 # Sanity check
                 if has_error_dy == True and not len(ty) == len(tdy):

src/sas/sascalc/dataloader/readers/cansas_reader.py

@@ -1177 +1177 @@
             written = written | self.write_node(pix, "z", item.pixel_size.z,
                                                 {"unit": item.pixel_size_unit})
-            written = written | self.write_node(det, "slit_length",
-                                                item.slit_length,
-                                                {"unit": item.slit_length_unit})
             if written == True:
                 self.append(pix, det)
+            self.write_node(det, "slit_length", item.slit_length,
+                {"unit": item.slit_length_unit})
+
 
     def _write_process_notes(self, datainfo, entry_node):

src/sas/sascalc/dataloader/readers/cansas_reader_HDF5.py

@@ -23 +23 @@
 
     Any number of SASdata sets may be present in a SASentry and the data within can be either 1D I(Q) or 2D I(Qx, Qy).
+<<<<<<< HEAD
+=======
+
+    Also supports reading NXcanSAS formatted HDF5 files
+>>>>>>> master
 
     :Dependencies:
@@ -76 +81 @@
                 ## Add the last data set to the list of outputs
                 self.add_data_set()
+                ## Close the data file
+                self.raw_data.close()
         ## Return data set(s)
         return self.output
@@ -189 +196 @@
 
                     ## Sample Information
-                    elif key == u'Title' and self.parent_class == u'SASsample':
+                    elif key == u'Title' and self.parent_class == u'SASsample': # CanSAS 2.0 format
+                        self.current_datainfo.sample.name = data_point
+                    elif key == u'ID' and self.parent_class == u'SASsample': # NXcanSAS format
                         self.current_datainfo.sample.name = data_point
                     elif key == u'thickness' and self.parent_class == u'SASsample':
@@ -213 +222 @@
                     elif key == u'name' and self.parent_class == u'SASprocess':
                         self.process.name = data_point
-                    elif key == u'Title' and self.parent_class == u'SASprocess':
-                        self.process.name = data_point
                     elif key == u'description' and self.parent_class == u'SASprocess':
                         self.process.description = data_point
@@ -230 +237 @@
                         self.trans_spectrum.wavelength.append(data_point)
 
-                    ## Other Information
+                    ## Source
                     elif key == u'wavelength' and self.parent_class == u'SASdata':
                         self.current_datainfo.source.wavelength = data_point
-                        self.current_datainfo.source.wavelength.unit = unit
+                        self.current_datainfo.source.wavelength_unit = unit
+                    elif key == u'incident_wavelength' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.wavelength = data_point
+                        self.current_datainfo.source.wavelength_unit = unit
+                    elif key == u'wavelength_max' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.wavelength_max = data_point
+                        self.current_datainfo.source.wavelength_max_unit = unit
+                    elif key == u'wavelength_min' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.wavelength_min = data_point
+                        self.current_datainfo.source.wavelength_min_unit = unit
+                    elif key == u'wavelength_spread' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.wavelength_spread = data_point
+                        self.current_datainfo.source.wavelength_spread_unit = unit
+                    elif key == u'beam_size_x' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.beam_size.x = data_point
+                        self.current_datainfo.source.beam_size_unit = unit
+                    elif key == u'beam_size_y' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.beam_size.y = data_point
+                        self.current_datainfo.source.beam_size_unit = unit
+                    elif key == u'beam_shape' and self.parent_class == u'SASsource':
+                        self.current_datainfo.source.beam_shape = data_point
                     elif key == u'radiation' and self.parent_class == u'SASsource':
                         self.current_datainfo.source.radiation = data_point

src/sas/sascalc/dataloader/readers/xml_reader.py

@@ -70 +70 @@
             self.xmldoc = etree.parse(self.xml, parser=PARSER)
             self.xmlroot = self.xmldoc.getroot()
+        except etree.XMLSyntaxError as xml_error:
+            logging.info(xml_error)
+        except Exception:
+            self.xml = None
+            self.xmldoc = None
+            self.xmlroot = None
+
+    def set_xml_string(self, tag_soup):
+        """
+        Set an XML string as the working XML.
+
+        :param tag_soup: XML formatted string
+        """
+        try:
+            self.xml = tag_soup
+            self.xmldoc = tag_soup
+            self.xmlroot = etree.fromstring(tag_soup)
         except etree.XMLSyntaxError as xml_error:
             logging.info(xml_error)