Source code for sas.perspectives.invariant.invariant_state

"""
"""

#import time
import os
import sys
import logging
import copy
import sas.dataloader
#from xml.dom.minidom import parse
from lxml import etree
from sas.dataloader.readers.cansas_reader import Reader as CansasReader
from sas.dataloader.readers.cansas_reader import get_content
from sas.guiframe.utils import format_number
from sas.guiframe.gui_style import GUIFRAME_ID
from sas.guiframe.dataFitting import Data1D

INVNODE_NAME = 'invariant'
CANSAS_NS = "cansas1d/1.0"

# default state
list = {'file': 'None',
        'compute_num':0,
        'state_num':0,
        'is_time_machine':False,
        'background_tcl':0.0,
        'scale_tcl':1.0,
        'contrast_tcl':1.0,
        'porod_constant_tcl':'',
        'npts_low_tcl':10,
        'npts_high_tcl':10,
        'power_high_tcl':4.0,
        'power_low_tcl': 4.0,
        'enable_high_cbox':False,
        'enable_low_cbox':False,
        'guinier': True,
        'power_law_high': False,
        'power_law_low': False,
        'fit_enable_high': False,
        'fit_enable_low': False,
        'fix_enable_high':True,
        'fix_enable_low':True,
        'volume_tcl':'',
        'volume_err_tcl':'',
        'surface_tcl':'',
        'surface_err_tcl':''}
# list of states: This list will be filled as panel 
# init and the number of states increases
state_list = {}
bookmark_list = {}
# list of input parameters (will be filled up on panel init) used by __str__ 
input_list = {'background_tcl':0,
        'scale_tcl':0,
        'contrast_tcl':0,
        'porod_constant_tcl':'',
        'npts_low_tcl':0,
        'npts_high_tcl':0,
        'power_high_tcl':0,
        'power_low_tcl': 0}  
# list of output parameters (order sensitive) used by __str__    
output_list = [["qstar_low",      "Q* from low Q extrapolation [1/(cm*A)]"],
               ["qstar_low_err",             "dQ* from low Q extrapolation"],
               ["qstar_low_percent",  "Q* percent from low Q extrapolation"],
               ["qstar",              "Q* from data [1/(cm*A)]"],
               ["qstar_err",                                "dQ* from data"],
               ["qstar_percent",                     "Q* percent from data"],
               ["qstar_high",    "Q* from high Q extrapolation [1/(cm*A)]"],
               ["qstar_high_err",           "dQ* from high Q extrapolation"],
               ["qstar_high_percent", "Q* percent from low Q extrapolation"],
               ["qstar_total",         "total Q* [1/(cm*A)]"],
               ["qstar_total_err",                              "total dQ*"],
               ["volume",                                 "volume fraction"],
               ["volume_err",                       "volume fraction error"],
               ["surface",                               "specific surface"],
               ["surface_err",                     "specific surface error"]]

   

[docs]class InvariantState(object): """ Class to hold the state information of the InversionControl panel. """ def __init__(self): """ Default values """ # Input self.file = None self.data = Data1D(x=[], y=[], dx=None, dy=None) self.theory_lowQ = Data1D(x=[], y=[], dy=None) self.theory_lowQ.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM self.theory_highQ = Data1D(x=[], y=[], dy=None) self.theory_highQ.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM #self.is_time_machine = False self.saved_state = list self.state_list = state_list self.bookmark_list = bookmark_list self.input_list = input_list self.output_list = output_list self.compute_num = 0 self.state_num = 0 self.timestamp = ('00:00:00', '00/00/0000') self.container = None #plot image self.wximbmp = None # report_html strings import sas.perspectives.invariant as invariant path = invariant.get_data_path(media='media') path_report_html = os.path.join(path,"report_template.html") html_template = open(path_report_html,"r") self.template_str = html_template.read() self.report_str = self.template_str #self.report_str_save = None html_template.close() def __str__(self): """ Pretty print : return: string representing the state """ # Input string compute_num = self.saved_state['compute_num'] compute_state = self.state_list[str(compute_num)] my_time, date = self.timestamp file_name = self.file state_num = int(self.saved_state['state_num']) state = "\n[Invariant computation for %s: " % file_name state += "performed at %s on %s] \n" % (my_time, date) state += "State No.: %d \n" % state_num state += "\n=== Inputs ===\n" # text ctl general inputs ( excluding extrapolation text ctl) for key, value in self.input_list.iteritems(): if value == '': continue key_split = key.split('_') max_ind = len(key_split)-1 if key_split[max_ind] == 'tcl': name = "" if key_split[1] == 'low' or key_split[1] == 'high': continue for ind in range(0, max_ind): name += " %s" % key_split[ind] state += "%s: %s\n" % (name.lstrip(" "), value) # other input parameters extra_lo = compute_state['enable_low_cbox'] if compute_state['enable_low_cbox']: if compute_state['guinier']: extra_lo = 'Guinier' else: extra_lo = 'Power law' extra_hi = compute_state['enable_high_cbox'] if compute_state['enable_high_cbox']: extra_hi = 'Power law' state += "\nExtrapolation: High=%s; Low=%s\n" %(extra_hi, extra_lo) low_off = False high_off = False for key, value in self.input_list.iteritems(): key_split = key.split('_') max_ind = len(key_split) - 1 if key_split[max_ind] == 'tcl': name = "" # check each buttons whether or not ON or OFF if key_split[1] == 'low' or key_split[1] == 'high': if not compute_state['enable_low_cbox'] and \ key_split[max_ind-1] == 'low': low_off = True continue elif not compute_state['enable_high_cbox'] and \ key_split[max_ind-1] == 'high': high_off = True continue elif extra_lo == 'Guinier' and key_split[0] == 'power' and \ key_split[max_ind-1] == 'low': continue for ind in range(0, max_ind): name += " %s" % key_split[ind] name = name.lstrip(" ") if name == "power low" : if compute_state['fix_enable_low']: name += ' (Fixed)' else: name += ' (Fitted)' if name == "power high" : if compute_state['fix_enable_high']: name += ' (Fixed)' else: name += ' (Fitted)' state += "%s: %s\n" % (name, value) # Outputs state += "\n=== Outputs ===" for item in output_list: item_split = item[0].split('_') # Exclude the extrapolation that turned off if len(item_split) > 1: if low_off and item_split[1] == 'low': continue if high_off and item_split[1] == 'high': continue max_ind = len(item_split) - 1 value = None try: # Q* outputs exec "value = self.container.%s\n" % item[0] except: # other outputs than Q* name = item[0] + "_tcl" if name in self.saved_state.keys(): exec "value = self.saved_state['%s']" % name # Exclude the outputs w/'' if value == '': continue # Error outputs if item_split[max_ind] == 'err': state += "+- %s " % format_number(value) # Percentage outputs elif item_split[max_ind] == 'percent': try: value = float(value) * 100 except: pass state += "(%s %s)" % (format_number(value), '%') # Outputs else: state += "\n%s: %s " % (item[1], format_number(value, high=True)) # Include warning msg if self.container is not None: state += "\n\nNote:\n" + self.container.warning_msg return state
[docs] def clone_state(self): """ deepcopy the state """ return copy.deepcopy(self.saved_state)
[docs] def toXML(self, file="inv_state.inv", doc=None, entry_node=None): """ Writes the state of the InversionControl panel to file, as XML. Compatible with standalone writing, or appending to an already existing XML document. In that case, the XML document is required. An optional entry node in the XML document may also be given. : param file: file to write to : param doc: XML document object [optional] : param entry_node: XML node within the XML document at which we will append the data [optional] """ # TODO: Get this to work from xml.dom.minidom import getDOMImplementation import time timestamp = time.time() # Check whether we have to write a standalone XML file if doc is None: impl = getDOMImplementation() doc_type = impl.createDocumentType(INVNODE_NAME, "1.0", "1.0") newdoc = impl.createDocument(None, INVNODE_NAME, doc_type) top_element = newdoc.documentElement else: # We are appending to an existing document newdoc = doc top_element = newdoc.createElement(INVNODE_NAME) if entry_node is None: newdoc.documentElement.appendChild(top_element) else: entry_node.appendChild(top_element) attr = newdoc.createAttribute("version") attr.nodeValue = '1.0' top_element.setAttributeNode(attr) # File name element = newdoc.createElement("filename") if self.file != None and self.file != '': element.appendChild(newdoc.createTextNode(str(self.file))) else: element.appendChild(newdoc.createTextNode(str(file))) top_element.appendChild(element) element = newdoc.createElement("timestamp") element.appendChild(newdoc.createTextNode(time.ctime(timestamp))) attr = newdoc.createAttribute("epoch") attr.nodeValue = str(timestamp) element.setAttributeNode(attr) top_element.appendChild(element) # Current state state = newdoc.createElement("state") top_element.appendChild(state) for name,value in self.saved_state.iteritems(): element = newdoc.createElement(str(name)) element.appendChild(newdoc.createTextNode(str(value))) state.appendChild(element) # State history list history = newdoc.createElement("history") top_element.appendChild(history) for name, value in self.state_list.iteritems(): history_element = newdoc.createElement('state_' + str(name)) for state_name,state_value in value.iteritems(): state_element = newdoc.createElement(str(state_name)) child = newdoc.createTextNode(str(state_value)) state_element.appendChild(child) history_element.appendChild(state_element) #history_element.appendChild(state_list_element) history.appendChild(history_element) # Bookmarks bookmark_list[self.bookmark_num] = [\ #my_time,date,state,comp_state] bookmark = newdoc.createElement("bookmark") top_element.appendChild(bookmark) item_list = ['time','date','state','comp_state'] for name, value_list in self.bookmark_list.iteritems(): element = newdoc.createElement('mark_'+ str(name)) _,date,state,comp_state = value_list time_element = newdoc.createElement('time') time_element.appendChild(newdoc.createTextNode(str(value_list[0]))) date_element = newdoc.createElement('date') date_element.appendChild(newdoc.createTextNode(str(value_list[1]))) state_list_element = newdoc.createElement('state') comp_state_list_element = newdoc.createElement('comp_state') for state_name, state_value in value_list[2].iteritems(): state_element = newdoc.createElement(str(state_name)) child = newdoc.createTextNode(str(state_value)) state_element.appendChild(child) state_list_element.appendChild(state_element) for comp_name, comp_value in value_list[3].iteritems(): comp_element = newdoc.createElement(str(comp_name)) comp_element.appendChild(newdoc.createTextNode(str(comp_value))) comp_state_list_element.appendChild(comp_element) element.appendChild(time_element) element.appendChild(date_element) element.appendChild(state_list_element) element.appendChild(comp_state_list_element) bookmark.appendChild(element) # Save the file if doc is None: fd = open('test000', 'w') fd.write(newdoc.toprettyxml()) fd.close() return None else: return newdoc
[docs] def fromXML(self, file=None, node=None): """ Load invariant states from a file : param file: .inv file : param node: node of a XML document to read from """ if file is not None: msg = "InvariantSate no longer supports non-CanSAS" msg += " format for invariant files" raise RuntimeError, msg if node.get('version')\ and node.get('version') == '1.0': # Get file name entry = get_content('ns:filename', node) if entry is not None: file_name = entry.text.strip() # Get time stamp entry = get_content('ns:timestamp', node) if entry is not None and entry.get('epoch'): try: timestamp = (entry.get('epoch')) except: msg = "InvariantSate.fromXML: Could not read" msg += " timestamp\n %s" % sys.exc_value logging.error(msg) # Parse bookmarks entry_bookmark = get_content('ns:bookmark', node) for ind in range(1, len(entry_bookmark) + 1): temp_state = {} temp_bookmark = {} entry = get_content('ns:mark_%s' % ind, entry_bookmark) if entry is not None: my_time = get_content('ns:time', entry) val_time = str(my_time.text.strip()) date = get_content('ns:date', entry) val_date = str(date.text.strip()) state_entry = get_content('ns:state', entry) for item in list: input_field = get_content('ns:%s' % item, state_entry) val = str(input_field.text.strip()) if input_field is not None: try: exec "temp_state['%s'] = %s" % (item, val) except: exec "temp_state['%s'] = '%s'" % (item, val) comp_entry = get_content('ns:comp_state', entry) for item in list: input_field = get_content('ns:%s' % item, comp_entry) val = str(input_field.text.strip()) if input_field is not None: try: exec "temp_bookmark['%s'] = %s" % (item, val) except: exec "temp_bookmark['%s'] = '%s'" % (item, val) try: cmd = "self.bookmark_list[%s] = [val_time," cmd += "val_date,temp_state,temp_bookmark]" exec cmd % ind except: raise "missing components of bookmarks..." # Parse histories entry_history = get_content('ns:history', node) for ind in range(0, len(entry_history)): temp_state = {} entry = get_content('ns:state_%s' % ind, entry_history) if entry is not None: for item in list: input_field = get_content('ns:%s' % item, entry ) val = str(input_field.text.strip()) if input_field is not None: try: exec "temp_state['%s'] = %s" % (item, val) except: exec "temp_state['%s'] = '%s'" % (item, val) finally: exec "self.state_list['%s'] = temp_state" % ind # Parse current state (ie, saved_state) entry = get_content('ns:state', node) if entry is not None: for item in list: input_field = get_content('ns:%s' % item, entry) val = str(input_field.text.strip()) if input_field is not None: self.set_saved_state(name=item, value=val) self.file = file_name
[docs] def set_report_string(self): """ Get the values (strings) from __str__ for report """ strings = self.__str__() # default string values for num in range (1, 19): exec "s_%s = 'NA'" % str(num) lines = strings.split('\n') # get all string values from __str__() for line in range(0, len(lines)): if line == 1: s_1 = lines[1] elif line == 2: s_2 = lines[2] else: item = lines[line].split(':') item[0] = item[0].strip() if item[0] == "scale": s_3 = item[1] elif item[0] == "porod constant": s_4 = item[1] elif item[0] == "background": s_5 = item[1] elif item[0] == "contrast": s_6 = item[1] elif item[0] == "Extrapolation": extra = item[1].split(";") bool_0 = extra[0].split("=") bool_1 = extra[1].split("=") s_8 = " " + bool_0[0] + "Q region = " + bool_0[1] s_7 = " " + bool_1[0] + "Q region = " + bool_1[1] elif item[0] == "npts low": s_9 = item[1] elif item[0] == "npts high": s_10 = item[1] elif item[0] == "volume fraction": val=item[1].split("+-")[0].strip() error = item[1].split("+-")[1].strip() s_17 = val + " ± " + error elif item[0] == "specific surface": val = item[1].split("+-")[0].strip() error = item[1].split("+-")[1].strip() s_18 = val + " ± " + error elif item[0].split("(")[0].strip() == "power low": s_11 = item[0]+" ="+item[1] elif item[0].split("(")[0].strip() == "power high": s_12 = item[0]+" ="+item[1] elif item[0].split("[")[0].strip() == "Q* from low Q extrapolation": #looks messy but this way the symbols +_ and % work on html val = item[1].split("+-")[0].strip() error = item[1].split("+-")[1].strip() err = error.split("%")[0].strip() percent = error.split("%")[1].strip() s_13 = val + " ± " + err + "&#37" + percent elif item[0].split("[")[0].strip() == "Q* from data": val = item[1].split("+-")[0].strip() error = item[1].split("+-")[1].strip() err = error.split("%")[0].strip() percent = error.split("%")[1].strip() s_14 = val + " ± " + err + "&#37" + percent elif item[0].split("[")[0].strip() == "Q* from high Q extrapolation": val = item[1].split("+-")[0].strip() error = item[1].split("+-")[1].strip() err = error.split("%")[0].strip() percent = error.split("%")[1].strip() s_15 = val + " ± " + err + "&#37" + percent elif item[0].split("[")[0].strip() == "total Q*": val = item[1].split("+-")[0].strip() error = item[1].split("+-")[1].strip() s_16 = val + " ± " + error else: continue s_1 = self._check_html_format(s_1) file_name = self._check_html_format(self.file) # make plot image self.set_plot_state(extra_high=bool_0[1],extra_low=bool_1[1]) # get ready for report with setting all the html strings self.report_str = str(self.template_str) % (s_1, s_2, s_3, s_4, s_5, s_6, s_7, s_8, s_9, s_10, s_11, s_12, s_13, s_14, s_15, s_16, s_17, s_18, file_name, "%s")
def _check_html_format(self, name): """ Check string '%' for html format """ if name.count('%'): name = name.replace('%', '&#37') return name
[docs] def set_saved_state(self, name, value): """ Set the state list : param name: name of the state component : param value: value of the state component """ rb_list = [['power_law_low','guinier'], ['fit_enable_low','fix_enable_low'], ['fit_enable_high','fix_enable_high']] try: if value == None or value.lstrip().rstrip() == '': exec "self.%s = '%s'" % (name, value) exec "self.saved_state['%s'] = '%s'" % (name, value) else: exec 'self.%s = %s' % (name, value) exec "self.saved_state['%s'] = %s" % (name, value) # set the count part of radio button clicked # False for the saved_state for title, content in rb_list: if name == title: name = content value = False elif name == content: name = title value = False exec "self.saved_state['%s'] = '%s'" % (name, value) self.state_num = self.saved_state['state_num'] except: pass
[docs] def set_plot_state(self, extra_high=False, extra_low=False): """ Build image state that wx.html understand by plotting, putting it into wx.FileSystem image object : extrap_high,extra_low: low/high extrapolations are possible extra-plots """ # some imports import wx import matplotlib.pyplot as plt from matplotlib.backends.backend_agg import FigureCanvasAgg #we use simple plot, not plotpanel #make matlab figure fig = plt.figure() fig.set_facecolor('w') graph = fig.add_subplot(111) #data plot graph.errorbar(self.data.x, self.data.y, yerr=self.data.dy, fmt='o') #low Q extrapolation fit plot if not extra_low == 'False': graph.plot(self.theory_lowQ.x,self.theory_lowQ.y) #high Q extrapolation fit plot if not extra_high == 'False': graph.plot(self.theory_highQ.x,self.theory_highQ.y) graph.set_xscale("log", nonposx='clip') graph.set_yscale("log", nonposy='clip') graph.set_xlabel('$\\rm{Q}(\\AA^{-1})$', fontsize = 12) graph.set_ylabel('$\\rm{Intensity}(cm^{-1})$', fontsize = 12) canvas = FigureCanvasAgg(fig) #actually make image canvas.draw() #make python.Image object #size w, h = canvas.get_width_height() #convert to wx.Image wximg = wx.EmptyImage(w,h) #wxim.SetData(img.convert('RGB').tostring() ) wximg.SetData(canvas.tostring_rgb()) #get the dynamic image for the htmlwindow wximgbmp = wx.BitmapFromImage(wximg) #store the image in wx.FileSystem Object wx.FileSystem.AddHandler(wx.MemoryFSHandler()) # use wx.MemoryFSHandler self.imgRAM = wx.MemoryFSHandler() #AddFile, image can be retrieved with 'memory:filename' self.imgRAM.AddFile('img_inv.png', wximgbmp, wx.BITMAP_TYPE_PNG) self.wximgbmp = 'memory:img_inv.png' self.image = fig
[docs]class Reader(CansasReader): """ Class to load a .inv invariant file """ ## File type type_name = "Invariant" ## Wildcards type = ["Invariant file (*.inv)|*.inv", "SASView file (*.svs)|*.svs"] ## List of allowed extensions ext = ['.inv', '.INV', '.svs', 'SVS'] def __init__(self, call_back, cansas=True): """ Initialize the call-back method to be called after we load a file : param call_back: call-back method : param cansas: True = files will be written/read in CanSAS format False = write CanSAS format """ ## Call back method to be executed after a file is read self.call_back = call_back ## CanSAS format flag self.cansas = cansas self.state = None
[docs] def read(self, path): """ Load a new invariant state from file : param path: file path : return: None """ if self.cansas == True: return self._read_cansas(path) else: return self._read_standalone(path)
def _read_standalone(self, path): """ Load a new invariant state from file. The invariant node is assumed to be the top element. : param path: file path : return: None """ # Read the new state from file state = InvariantState() state.fromXML(file=path) # Call back to post the new state self.call_back(state) return None def _parse_state(self, entry): """ Read an invariant result from an XML node : param entry: XML node to read from : return: InvariantState object """ state = None # Locate the invariant node try: nodes = entry.xpath('ns:%s' % INVNODE_NAME, namespaces={'ns': CANSAS_NS}) # Create an empty state if nodes != []: state = InvariantState() state.fromXML(node=nodes[0]) except: msg = "XML document does not contain invariant" msg += " information.\n %s" % sys.exc_value logging.info(msg) return state def _read_cansas(self, path): """ Load data and invariant information from a CanSAS XML file. : param path: file path : return: Data1D object if a single SASentry was found, or a list of Data1D objects if multiple entries were found, or None of nothing was found : raise RuntimeError: when the file can't be opened : raise ValueError: when the length of the data vectors are inconsistent """ output = [] if os.path.isfile(path): basename = os.path.basename(path) root, extension = os.path.splitext(basename) if extension.lower() in self.ext or \ extension.lower() == '.xml': tree = etree.parse(path, parser=etree.ETCompatXMLParser()) # Check the format version number # Specifying the namespace will take care of # the file format version root = tree.getroot() entry_list = root.xpath('/ns:SASroot/ns:SASentry', namespaces={'ns': CANSAS_NS}) for entry in entry_list: sas_entry, _ = self._parse_entry(entry) invstate = self._parse_state(entry) #invstate could be None when .svs file is loaded #in this case, skip appending to output if invstate != None: sas_entry.meta_data['invstate'] = invstate sas_entry.filename = invstate.file output.append(sas_entry) else: raise RuntimeError, "%s is not a file" % path # Return output consistent with the loader's api if len(output) == 0: return None elif len(output) == 1: # Call back to post the new state self.state = output[0].meta_data['invstate'] self.call_back(state=output[0].meta_data['invstate'], datainfo = output[0]) return output[0] else: return output
[docs] def get_state(self): return self.state
[docs] def write(self, filename, datainfo=None, invstate=None): """ Write the content of a Data1D as a CanSAS XML file : param filename: name of the file to write : param datainfo: Data1D object : param invstate: InvariantState object """ # Sanity check if self.cansas == True: doc = self.write_toXML(datainfo,invstate) # Write the XML document fd = open(filename, 'w') fd.write(doc.toprettyxml()) fd.close() else: invstate.toXML(file=filename)
[docs] def write_toXML(self, datainfo=None, state=None): """ Write toXML, a helper for write() : return: xml doc """ if datainfo is None: datainfo = sas.dataloader.data_info.Data1D(x=[], y=[]) elif not issubclass(datainfo.__class__, sas.dataloader.data_info.Data1D): msg = "The cansas writer expects a Data1D" msg += " instance: %s" % str(datainfo.__class__.__name__) raise RuntimeError, msg #make sure title and data run is filled up. if datainfo.title == None or datainfo.title == '': datainfo.title = datainfo.name if datainfo.run_name == None or datainfo.run_name == {}: datainfo.run = [str(datainfo.name)] datainfo.run_name[0] = datainfo.name # Create basic XML document doc, sasentry = self._to_xml_doc(datainfo) # Add the invariant information to the XML document if state is not None: doc = state.toXML(datainfo.name,doc=doc, entry_node=sasentry) return doc