################################################################################ #This software was developed by the University of Tennessee as part of the #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) #project funded by the US National Science Foundation. # #See the license text in license.txt # #copyright 2009, University of Tennessee ################################################################################ import time import os import sys import copy import logging import numpy import xml.dom.minidom from xml.dom.minidom import parse from lxml import etree import sans.dataloader from sans.dataloader.readers.cansas_reader import Reader as CansasReader from sans.dataloader.readers.cansas_reader import get_content, write_node from sans.dataloader.data_info import Data2D, Detector #Information to read/write state as xml FITTING_NODE_NAME = 'fitting_plug_in' CANSAS_NS = "cansas1d/1.0" list_of_data_attributes = [["is_data", "is_data", "bool"], ["group_id", "data_group_id", "string"], ["data_name", "data_name", "string"], ["data_id", "data_id", "string"], ["name", "name", "string"], ["data_name", "data_name", "string"]] list_of_state_attributes = [["engine_type", "engine_type", "string"], ["qmin", "qmin", "float"], ["qmax", "qmax", "float"], ["npts", "npts", "float"], ["shape_rbutton", "shape_rbutton", "bool"], ["shape_indep_rbutton", "shape_indep_rbutton", "bool"], ["plugin_rbutton", "plugin_rbutton","bool"], ["struct_rbutton", "struct_rbutton", "bool"], ["formfactorcombobox", "formfactorcombobox", "float"], ["structurecombobox", "structurecombobox", "float"], ["multi_factor","multi_factor","float"], ["enable_smearer","enable_smearer","bool"], ["disable_smearer","disable_smearer","bool"], ["pinhole_smearer","pinhole_smearer","bool"], ["slit_smearer","slit_smearer","bool"], ["enable_disp","enable_disp","bool"], ["disable_disp","disable_disp","bool"], ["slit_smearer","slit_smearer","bool"], ["enable2D","enable2D","bool"], ["cb1","cb1","bool"], ["tcChi","tcChi","float"], ["smearer", "smearer", "float"], ["smear_type","smear_type", "string"], ["dq_l", "dq_l", "string"], ["dq_r","dq_r", "string"]] list_of_model_attributes = [["values", "values"], ["weights", "weights"]] list_of_obj_dic = [["disp_obj_dict", "_disp_obj_dict", "string"]] list_of_state_parameters = [["parameters", "parameters"] , ["str_parameters", "str_parameters"] , ["orientation_parameters", "orientation_params"], ["dispersity_parameters", "orientation_params_disp"], ["fixed_param", "fixed_param"], ["fittable_param","fittable_param"]] list_of_data_2d_attr = [["xmin", "xmin","float"], ["xmax","xmax","float"], ["ymin","ymin","float"], ["ymax","ymax","float"], ["_xaxis","_xaxis", "string"], ["_xunit", "_xunit", "string"], ["_yaxis","_yaxis","string"], ["_yunit","_yunit","string"], ["_zaxis","_zaxis","string"], ["_zunit","_zunit","string"]] list_of_data2d_values = [["qx_data","qx_data","float"], ["qy_data","qy_data","float"], ["dqx_data","dqx_data","float"], ["dqy_data","dqy_data","float"], ["data","data","float"], ["q_data","q_data","float"], ["err_data","err_data","float"], ["mask","mask","bool"]] def parse_entry_helper( node, item): """ Create a numpy list from value extrated from the node :param node: node from each the value is stored :param item: list name of three strings.the two first are name of data attribute and the third one is the type of the value of that attribute. type can be string, float, bool, etc. : return: numpy array """ if node is not None: if item[2] == "string": return str(node.get(item[0]).strip()) elif item[2] == "bool": try: return node.get(item[0]).strip() == "True" except: return None else: try: return float(node.get(item[0])) except: return None class PageState(object): """ Contains information to reconstruct a page of the fitpanel. """ def __init__(self, parent=None, model=None, data=None): """ Initialize the current state :param model: a selected model within a page :param data: """ self.file = None #Time of state creation self.timestamp = time.time() ## Data member to store the dispersion object created self._disp_obj_dict = {} #------------------------ #Data used for fitting self.data = data # model data self.theory_data = None #Is 2D self.is_2D = False self.images = None #save additional information on data that dataloader.reader does not read self.is_data = None self.data_name = "" if self.data is not None: self.data_name = self.data.name self.data_id = None if self.data is not None and hasattr(self.data, "id"): self.data_id = self.data.id self.data_group_id = None if self.data is not None and hasattr(self.data, "group_id"): self.data_group_id = self.data.group_id ## reset True change the state of exsiting button self.reset = False #engine type self.engine_type = None # flag to allow data2D plot self.enable2D = False # model on which the fit would be performed self.model = model #list of process done to model self.process = [] #fit page manager self.manager = None #Store the parent of this panel parent # For this application fitpanel is the parent self.parent = parent # Event_owner is the owner of model event self.event_owner = None ##page name self.page_name = "" # Contains link between model ,all its parameters, and panel organization self.parameters = [] # String parameter list that can not be fitted self.str_parameters = [] # Contains list of parameters that cannot be fitted and reference to #panel objects self.fixed_param = [] # Contains list of parameters with dispersity and reference to #panel objects self.fittable_param = [] ## orientation parameters self.orientation_params = [] ## orientation parmaters for gaussian dispersity self.orientation_params_disp = [] ## smearer info self.smearer = None self.smear_type = None self.dq_l = None self.dq_r = None #list of dispersion paramaters self.disp_list =[] if self.model is not None: self.disp_list = self.model.getDispParamList() self.disp_cb_dict = {} self.values = {} self.weights = {} #contains link between a model and selected parameters to fit self.param_toFit = [] ##dictionary of model type and model class self.model_list_box = None ## save the state of the context menu self.saved_states = {} ## save selection of combobox self.formfactorcombobox = None self.structurecombobox = None ## radio box to select type of model self.shape_rbutton = False self.shape_indep_rbutton = False self.struct_rbutton = False self.plugin_rbutton = False ## the indice of the current selection self.disp_box = 0 ## Qrange ## Q range self.qmin = 0.001 self.qmax = 0.1 #reset data range self.qmax_x = None self.qmin_x = None self.npts = None self.name = "" self.multi_factor = None ## enable smearering state self.enable_smearer = False self.disable_smearer = True self.pinhole_smearer = False self.slit_smearer = False ## disperity selection self.enable_disp = False self.disable_disp = True ## state of selected all check button self.cb1 = False ## store value of chisqr self.tcChi = None def clone(self): """ Create a new copy of the current object """ model = None if self.model is not None: model = self.model.clone() model.name = self.model.name obj = PageState(self.parent, model=model) obj.file = copy.deepcopy(self.file) obj.data = copy.deepcopy(self.data) if self.data is not None: self.data_name = self.data.name obj.data_name = self.data_name obj.is_data = self.is_data obj.model_list_box = copy.deepcopy(self.model_list_box) obj.engine_type = copy.deepcopy(self.engine_type) obj.formfactorcombobox = self.formfactorcombobox obj.structurecombobox = self.structurecombobox obj.shape_rbutton = self.shape_rbutton obj.shape_indep_rbutton = self.shape_indep_rbutton obj.struct_rbutton = self.struct_rbutton obj.plugin_rbutton = self.plugin_rbutton obj.manager = self.manager obj.event_owner = self.event_owner obj.disp_list = copy.deepcopy(self.disp_list) obj.enable2D = copy.deepcopy(self.enable2D) obj.parameters = copy.deepcopy(self.parameters) obj.str_parameters = copy.deepcopy(self.str_parameters) obj.fixed_param = copy.deepcopy(self.fixed_param) obj.fittable_param = copy.deepcopy(self.fittable_param) obj.orientation_params = copy.deepcopy(self.orientation_params) obj.orientation_params_disp = copy.deepcopy(self.orientation_params_disp) obj.enable_disp = copy.deepcopy(self.enable_disp) obj.disable_disp = copy.deepcopy(self.disable_disp) obj.tcChi = self.tcChi if len(self._disp_obj_dict)>0: for k , v in self._disp_obj_dict.iteritems(): obj._disp_obj_dict[k]= v if len(self.disp_cb_dict)>0: for k , v in self.disp_cb_dict.iteritems(): obj.disp_cb_dict[k]= v if len(self.values)>0: for k , v in self.values.iteritems(): obj.values[k] = v if len(self.weights)>0: for k , v in self.weights.iteritems(): obj.weights[k] = v obj.enable_smearer = copy.deepcopy(self.enable_smearer) obj.disable_smearer = copy.deepcopy(self.disable_smearer) obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) obj.slit_smearer = copy.deepcopy(self.slit_smearer) obj.smear_type = copy.deepcopy(self.smear_type) obj.dq_l = copy.deepcopy(self.dq_l) obj.dq_r = copy.deepcopy(self.dq_r) obj.disp_box = copy.deepcopy(self.disp_box) obj.qmin = copy.deepcopy(self.qmin) obj.qmax = copy.deepcopy(self.qmax) obj.multi_factor = self.multi_factor obj.npts = copy.deepcopy(self.npts ) obj.cb1 = copy.deepcopy(self.cb1) obj.smearer = copy.deepcopy(self.smearer) for name, state in self.saved_states.iteritems(): copy_name = copy.deepcopy(name) copy_state = state.clone() obj.saved_states[copy_name]= copy_state return obj def _repr_helper(self, list, rep): """ Helper method to print a state """ for item in list: rep += "parameter name: %s \n"%str(item[1]) rep += "value: %s\n"%str(item[2]) rep += "selected: %s\n"%str(item[0]) rep += "error displayed : %s \n"%str(item[4][0]) rep += "error value:%s \n"%str(item[4][1]) rep += "minimum displayed : %s \n"%str(item[5][0]) rep += "minimum value : %s \n"%str(item[5][1]) rep += "maximum displayed : %s \n"%str(item[6][0]) rep += "maximum value : %s \n"%str(item[6][1]) rep += "parameter unit: %s\n\n"%str(item[7]) return rep def __repr__(self): """ output string for printing """ rep = "\nState name: %s\n"%self.file t = time.localtime(self.timestamp) time_str = time.strftime("%b %d %H;%M of %Y", t) rep += "State created on : %s\n"%time_str rep += "State form factor combobox selection: %s\n"%self.formfactorcombobox rep += "State structure factor combobox selection: %s\n"%self.structurecombobox rep += "is data : %s\n"%self.is_data rep += "data's name : %s\n"%self.data_name rep += "data's id : %s\n"%self.data_id rep += "model type (form factor) selected: %s\n"%self.shape_rbutton rep += "multi_factor : %s\n"% str(self.multi_factor) rep += "model type (shape independent) selected: %s\n"%self.shape_indep_rbutton rep += "model type (structure factor) selected: %s\n"%self.struct_rbutton rep += "model type (plug-in ) selected: %s\n"%self.plugin_rbutton rep += "data : %s\n"% str(self.data) rep += "Plotting Range: min: %s, max: %s, steps: %s\n"%(str(self.qmin), str(self.qmax),str(self.npts)) rep += "Dispersion selection : %s\n"%str(self.disp_box) rep += "Smearing enable : %s\n"%str(self.enable_smearer) rep += "Smearing disable : %s\n"%str(self.disable_smearer) rep += "Pinhole smearer enable : %s\n"%str(self.pinhole_smearer) rep += "Slit smearer enable : %s\n"%str(self.slit_smearer) rep += "Dispersity enable : %s\n"%str(self.enable_disp) rep += "Dispersity disable : %s\n"%str(self.disable_disp) rep += "Slit smearer enable: %s\n"%str(self.slit_smearer) rep += "2D enable : %s\n"%str(self.enable2D) rep += "All parameters checkbox selected: %s\n"%(self.cb1) rep += "Value of Chisqr : %s\n"%str(self.tcChi) rep += "Smear object : %s\n"%str(self.smearer) rep += "Smear type : %s\n"%(self.smear_type) rep += "dq_l : %s\n"%self.dq_l rep += "dq_r : %s\n"%self.dq_r rep += "model : %s\n\n"% str(self.model) temp_parameters = [] temp_fittable_param = [] if self.data.__class__.__name__ == "Data2D": self.is_2D = True else: self.is_2D = False if self.data is not None: if not self.is_2D: for item in self.parameters: if not item in self.orientation_params: temp_parameters.append(item) for item in self.fittable_param: if not item in self.orientation_params_disp: temp_fittable_param.append(item) else: temp_parameters = self.parameters temp_fittable_param = self.fittable_param rep += "number parameters(self.parameters): %s\n"%len(temp_parameters) rep = self._repr_helper( list=temp_parameters, rep=rep) rep += "number str_parameters(self.str_parameters): %s\n"%len(self.str_parameters) rep = self._repr_helper( list=self.str_parameters, rep=rep) rep += "number fittable_param(self.fittable_param): %s\n"%len(temp_fittable_param) rep = self._repr_helper( list=temp_fittable_param, rep=rep) """ if is_2D: rep += "number orientation parameters" rep += "(self.orientation_params): %s\n"%len(self.orientation_params) rep = self._repr_helper( list=self.orientation_params, rep=rep) rep += "number dispersity parameters" rep += "(self.orientation_params_disp): %s\n"%len(self.orientation_params_disp) rep = self._repr_helper( list=self.orientation_params_disp, rep=rep) """ return rep def set_report_string(self): """ Get the values (strings) from __str__ for report """ # Dictionary of teh report strings repo_time = "" model_name = "" title = "" title_name = "" file_name = "" param_string = "" paramval_string = "" chi2_string = "" multi_factor_string = "" q_range = "" strings = self.__repr__() lines = strings.split('\n') # get all string values from __str__() for line in lines: value = "" content = line.split(":") name = content[0] try: value = content[1] except: pass if name.count("State created on"): repo_time = "Created on " + value if name.count("parameter name"): val_name = value.split(".") if len(val_name) > 1: if val_name[1].count("width"): param_string += value + ',' else: continue else: param_string += value + ',' if name == "value": param_string += value + ',' if name == "error value": param_string += value + ',' if name == "parameter unit": param_string += value + ':' if name == "Value of Chisqr ": chi2 = ("Chi2/Npts = " + value) chi2_string = CENTRE % chi2 if name == "multi_factor ": muti_factor = ("muti_factor = " + value) muti_factor_string = CENTRE % muti_factor if name == "Title": if len(value.strip()) == 0: continue title = value + " [" + repo_time + "]" title_name = HEADER % title if name == "data ": try: file = ("File name:" + content[2]) file_name = CENTRE % file if len(title) == 0: title = content[2] + " [" + repo_time + "]" title_name = HEADER % title except: pass if name == "Plotting Range": try: q_range = content[1] + " = " + content[2] \ + " = " + content[3].split(",")[0] q_name = ("Q Range: " + q_range) q_range = CENTRE % q_name except: pass paramval = "" for lines in param_string.split(":"): line = lines.split(",") if len(lines) > 0: param = line[0] param += " = " + line[1] if len(line[2].split()) > 0 and not line[2].count("None"): param += " +- " + line[2] if len(line[3].split()) > 0 and not line[3].count("None"): param += " " + line[3] if not paramval.count(param): paramval += param + "\n" paramval_string += CENTRE % param + "\n" text_string = "\n\n\n" + title + "\n\n" + file + \ "\n" + q_name + \ "\n" + chi2 + \ "\n\n" + paramval title_name = self._check_html_format(title_name) file_name = self._check_html_format(file_name) title = self._check_html_format(title) html_string = title_name + "\n" + file_name + \ "\n" + q_range + \ "\n" + chi2_string + \ "\n" + ELINE + \ "\n" + paramval_string + \ "\n" + ELINE + \ "\n" + FEET_1 % title + \ "\n" + FEET_2 return html_string, text_string, title def _check_html_format(self, name): """ Check string '%' for html format """ if name.count('%'): name = name.replace('%', '%') return name def report(self, figs=None, canvases=None): """ Invoke report dialog panel : param figs: list of pylab figures [list] """ from report_dialog import ReportDialog # get the strings for report html_str, text_str, title = self.set_report_string() # Allow 2 figures to append if len(figs) == 1: add_str = FEET_3 elif len(figs) == 2: add_str = ELINE add_str += FEET_2 % ("%s") add_str += ELINE add_str += FEET_3 elif len(figs) > 2: add_str = ELINE add_str += FEET_2 % ("%s") add_str += ELINE add_str += FEET_2 % ("%s") add_str += ELINE add_str += FEET_3 else: add_str = "" # final report html strings report_str = html_str % ("%s") + add_str # make plot image images = self.set_plot_state(figs, canvases) report_list = [report_str, text_str, images ] dialog = ReportDialog(report_list, None, -1, "") dialog.ShowModal() def _toXML_helper(self, list, element, newdoc): """ Helper method to create xml file for saving state """ for item in list: sub_element = newdoc.createElement('parameter') sub_element.setAttribute('name', str(item[1])) sub_element.setAttribute('value', str(item[2])) sub_element.setAttribute('selected_to_fit', str(item[0])) sub_element.setAttribute('error_displayed', str(item[4][0])) sub_element.setAttribute('error_value', str(item[4][1])) sub_element.setAttribute('minimum_displayed', str(item[5][0])) sub_element.setAttribute('minimum_value', str(item[5][1])) sub_element.setAttribute('maximum_displayed', str(item[6][0])) sub_element.setAttribute('maximum_value', str(item[6][1])) sub_element.setAttribute('unit', str(item[7])) element.appendChild(sub_element) def toXML(self, file="fitting_state.fitv", 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] """ from xml.dom.minidom import getDOMImplementation # Check whether we have to write a standalone XML file if doc is None: impl = getDOMImplementation() doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) top_element = newdoc.documentElement else: # We are appending to an existing document newdoc = doc top_element = newdoc.createElement(FITTING_NODE_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 is not None: 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(self.timestamp))) attr = newdoc.createAttribute("epoch") attr.nodeValue = str(self.timestamp) element.setAttributeNode(attr) top_element.appendChild(element) # Inputs inputs = newdoc.createElement("Attributes") top_element.appendChild(inputs) if self.data is not None and hasattr(self.data, "group_id"): self.data_group_id = self.data.group_id if self.data is not None and hasattr(self.data, "is_data"): self.is_data = self.data.is_data if self.data is not None: self.data_name = self.data.name if self.data is not None and hasattr(self.data, "id"): self.data_id = self.data.id for item in list_of_data_attributes: element = newdoc.createElement(item[0]) exec "element.setAttribute(item[0], str(self.%s))" % (item[1]) inputs.appendChild(element) for item in list_of_state_attributes: element = newdoc.createElement(item[0]) exec "element.setAttribute(item[0], str(self.%s))" % (item[1]) inputs.appendChild(element) # For self.values ={ disp_param_name: [vals,...],...} # and for self.weights ={ disp_param_name: [weights,...],...} for item in list_of_model_attributes: element = newdoc.createElement(item[0]) exec "list = self.%s" % item[1] for key, value in list.iteritems(): sub_element = newdoc.createElement(key) sub_element.setAttribute('name', str(key)) for val in value: com = "sub_element.appendChild" com += "(newdoc.createTextNode(str(%s)))" exec com % val element.appendChild(sub_element) inputs.appendChild(element) # Create doc for the dictionary of self._disp_obj_dic for item in list_of_obj_dic: element = newdoc.createElement(item[0]) exec "list = self.%s" % item[1] for key, val in list.iteritems(): value = repr(val) sub_element = newdoc.createElement(key) sub_element.setAttribute('name', str(key)) sub_element.setAttribute('value', str(value)) element.appendChild(sub_element) inputs.appendChild(element) for item in list_of_state_parameters: element = newdoc.createElement(item[0]) com = "self._toXML_helper(list=self.%s," com += " element=element, newdoc=newdoc)" exec com % item[1] inputs.appendChild(element) # Save the file if doc is None: fd = open(file, 'w') fd.write(newdoc.toprettyxml()) fd.close() return None else: return newdoc.toprettyxml() def _fromXML_helper(self, node, list): """ Helper function to write state to xml """ for item in node: try: name = item.get('name') except: name = None try: value = item.get('value') except: value = None try: selected_to_fit = (item.get('selected_to_fit') == "True") except: selected_to_fit = None try: error_displayed = (item.get('error_displayed') == "True") except: error_displayed = None try: error_value = item.get('error_value') except: error_value = None try: minimum_displayed = (item.get('minimum_displayed')== "True") except: minimum_displayed = None try: minimum_value = item.get('minimum_value') except: minimum_value = None try: maximum_displayed = (item.get('maximum_displayed') == "True") except: maximum_displayed = None try: maximum_value = item.get('maximum_value') except: maximum_value = None try: unit = item.get('unit') except: unit = None list.append([selected_to_fit, name, value, "+/-", [error_displayed, error_value], [minimum_displayed,minimum_value], [maximum_displayed,maximum_value], unit]) def fromXML(self, file=None, node=None): """ Load fitting state from a file :param file: .fitv file :param node: node of a XML document to read from """ if file is not None: msg = "PageState no longer supports non-CanSAS" msg += " format for fitting 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: self.file = entry.text.strip() # Get time stamp entry = get_content('ns:timestamp', node) if entry is not None and entry.get('epoch'): try: self.timestamp = float(entry.get('epoch')) except: msg = "PageState.fromXML: Could not" msg += " read timestamp\n %s" % sys.exc_value logging.error(msg) # Parse fitting attributes entry = get_content('ns:Attributes', node) for item in list_of_data_attributes: node = get_content('ns:%s'%item[0], entry) try: exec "self.%s = parse_entry_helper(node, item)" % item[0] except: raise if entry is not None: for item in list_of_state_attributes: node = get_content('ns:%s' % item[0], entry) try: exec "self.%s = parse_entry_helper(node, item)" % \ str(item[0]) except: raise for item in list_of_state_parameters: node = get_content("ns:%s" % item[0], entry) exec "self._fromXML_helper(node=node, list=self.%s)" % \ item[1] # Recover _disp_obj_dict from xml file self._disp_obj_dict = {} for item in list_of_obj_dic: # Get node node = get_content("ns:%s" % item[0], entry) for attr in node: name = attr.get('name') val = attr.get('value') value = val.split(" instance")[0] disp_name = value.split("<")[1] try: # Try to recover disp_model object from strings com = "from sans.models.dispersion_models " com += "import %s as disp" com_name = disp_name.split(".")[3] exec com % com_name disp_model = disp() exec "self.%s['%s'] = com_name" % (item[1], name) except: pass # get self.values and self.weights dic. if exists for item in list_of_model_attributes: node = get_content("ns:%s" % item[0], entry) dic = {} list = [] for par in node: name = par.get('name') values = par.text.split('\n') # Get lines only with numbers for line in values: try: val= float(line) list.append(val) except: # pass if line is empty (it happens) pass dic[name] = numpy.array(list) exec "self.%s = dic" % item[1] def set_plot_state(self, figs, canvases): """ Build image state that wx.html understand by plotting, putting it into wx.FileSystem image object """ images = [] # some imports import wx # Reset memory self.imgRAM = None wx.MemoryFSHandler() # For no figures in the list, prepare empty plot if figs == None or len(figs) == 0: figs = [None] # Loop over the list of figures # use wx.MemoryFSHandler self.imgRAM = wx.MemoryFSHandler() for fig in figs: if figs != None: #fig.set_facecolor('w') ind = figs.index(fig) canvas = canvases[ind] #bmp = wx.BitmapDataObject() #bmp.SetBitmap(canvas.bitmap) #store the image in wx.FileSystem Object wx.FileSystem.AddHandler(wx.MemoryFSHandler()) # index of the fig ind = figs.index(fig) #AddFile, image can be retrieved with 'memory:filename' self.imgRAM.AddFile('img_fit%s.png' % ind , canvas.bitmap, wx.BITMAP_TYPE_PNG) #append figs images.append(fig) return images class Reader(CansasReader): """ Class to load a .fitv fitting file """ ## File type type_name = "Fitting" ## Wildcards type = ["Fitting files (*.fitv)|*.fitv" "SANSView file (*.svs)|*.svs"] ## List of allowed extensions ext=['.fitv', '.FITV', '.svs', 'SVS'] def __init__(self, call_back=None, cansas=True): CansasReader.__init__(self) """ 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 def get_state(self): return self.state def read(self, path): """ Load a new P(r) inversion state from file :param path: file path """ if self.cansas == True: return self._read_cansas(path) def _data2d_to_xml_doc(self, datainfo): """ Create an XML document to contain the content of a Data2D :param datainfo: Data2D object """ if not issubclass(datainfo.__class__, Data2D): raise RuntimeError, "The cansas writer expects a Data2D instance" doc = xml.dom.minidom.Document() main_node = doc.createElement("SASroot") main_node.setAttribute("version", self.version) main_node.setAttribute("xmlns", "cansas1d/%s" % self.version) main_node.setAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance") main_node.setAttribute("xsi:schemaLocation", "cansas1d/%s http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" % self.version) doc.appendChild(main_node) entry_node = doc.createElement("SASentry") main_node.appendChild(entry_node) write_node(doc, entry_node, "Title", datainfo.title) if datainfo is not None: write_node(doc, entry_node, "data_class", datainfo.__class__.__name__) for item in datainfo.run: runname = {} if datainfo.run_name.has_key(item) and len(str(datainfo.run_name[item]))>1: runname = {'name': datainfo.run_name[item] } write_node(doc, entry_node, "Run", item, runname) # Data info new_node = doc.createElement("SASdata") entry_node.appendChild(new_node) for item in list_of_data_2d_attr: element = doc.createElement(item[0]) exec "element.setAttribute(item[0], str(datainfo.%s))"%(item[1]) new_node.appendChild(element) for item in list_of_data2d_values: root_node = doc.createElement(item[0]) new_node.appendChild(root_node) exec "temp_list = datainfo.%s"%item[1] if temp_list is None or len(temp_list)== 0: element = doc.createElement(item[0]) exec "element.appendChild(doc.createTextNode(str(%s)))"%temp_list root_node.appendChild(element) else: for value in temp_list: element = doc.createElement(item[0]) exec "element.setAttribute(item[0], str(%s))"%value root_node.appendChild(element) # Sample info sample = doc.createElement("SASsample") if datainfo.sample.name is not None: sample.setAttribute("name", str(datainfo.sample.name)) entry_node.appendChild(sample) write_node(doc, sample, "ID", str(datainfo.sample.ID)) write_node(doc, sample, "thickness", datainfo.sample.thickness, {"unit":datainfo.sample.thickness_unit}) write_node(doc, sample, "transmission", datainfo.sample.transmission) write_node(doc, sample, "temperature", datainfo.sample.temperature, {"unit":datainfo.sample.temperature_unit}) for item in datainfo.sample.details: write_node(doc, sample, "details", item) pos = doc.createElement("position") written = write_node(doc, pos, "x", datainfo.sample.position.x, {"unit":datainfo.sample.position_unit}) written = written | write_node(doc, pos, "y", datainfo.sample.position.y, {"unit":datainfo.sample.position_unit}) written = written | write_node(doc, pos, "z", datainfo.sample.position.z, {"unit":datainfo.sample.position_unit}) if written == True: sample.appendChild(pos) ori = doc.createElement("orientation") written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, {"unit":datainfo.sample.orientation_unit}) written = written | write_node(doc, ori, "pitch", datainfo.sample.orientation.y, {"unit":datainfo.sample.orientation_unit}) written = written | write_node(doc, ori, "yaw", datainfo.sample.orientation.z, {"unit":datainfo.sample.orientation_unit}) if written == True: sample.appendChild(ori) # Instrument info instr = doc.createElement("SASinstrument") entry_node.appendChild(instr) write_node(doc, instr, "name", datainfo.instrument) # Source source = doc.createElement("SASsource") if datainfo.source.name is not None: source.setAttribute("name", str(datainfo.source.name)) instr.appendChild(source) write_node(doc, source, "radiation", datainfo.source.radiation) write_node(doc, source, "beam_shape", datainfo.source.beam_shape) size = doc.createElement("beam_size") if datainfo.source.beam_size_name is not None: size.setAttribute("name", str(datainfo.source.beam_size_name)) written = write_node(doc, size, "x", datainfo.source.beam_size.x, {"unit":datainfo.source.beam_size_unit}) written = written | write_node(doc, size, "y", datainfo.source.beam_size.y, {"unit":datainfo.source.beam_size_unit}) written = written | write_node(doc, size, "z", datainfo.source.beam_size.z, {"unit":datainfo.source.beam_size_unit}) if written == True: source.appendChild(size) write_node(doc, source, "wavelength", datainfo.source.wavelength, {"unit":datainfo.source.wavelength_unit}) write_node(doc, source, "wavelength_min", datainfo.source.wavelength_min, {"unit":datainfo.source.wavelength_min_unit}) write_node(doc, source, "wavelength_max", datainfo.source.wavelength_max, {"unit":datainfo.source.wavelength_max_unit}) write_node(doc, source, "wavelength_spread", datainfo.source.wavelength_spread, {"unit":datainfo.source.wavelength_spread_unit}) # Collimation for item in datainfo.collimation: coll = doc.createElement("SAScollimation") if item.name is not None: coll.setAttribute("name", str(item.name)) instr.appendChild(coll) write_node(doc, coll, "length", item.length, {"unit":item.length_unit}) for apert in item.aperture: ap = doc.createElement("aperture") if apert.name is not None: ap.setAttribute("name", str(apert.name)) if apert.type is not None: ap.setAttribute("type", str(apert.type)) coll.appendChild(ap) write_node(doc, ap, "distance", apert.distance, {"unit":apert.distance_unit}) size = doc.createElement("size") if apert.size_name is not None: size.setAttribute("name", str(apert.size_name)) written = write_node(doc, size, "x", apert.size.x, {"unit":apert.size_unit}) written = written | write_node(doc, size, "y", apert.size.y, {"unit":apert.size_unit}) written = written | write_node(doc, size, "z", apert.size.z, {"unit":apert.size_unit}) if written == True: ap.appendChild(size) # Detectors for item in datainfo.detector: det = doc.createElement("SASdetector") written = write_node(doc, det, "name", item.name) written = written | write_node(doc, det, "SDD", item.distance, {"unit":item.distance_unit}) written = written | write_node(doc, det, "slit_length", item.slit_length, {"unit":item.slit_length_unit}) if written == True: instr.appendChild(det) off = doc.createElement("offset") written = write_node(doc, off, "x", item.offset.x, {"unit":item.offset_unit}) written = written | write_node(doc, off, "y", item.offset.y, {"unit":item.offset_unit}) written = written | write_node(doc, off, "z", item.offset.z, {"unit":item.offset_unit}) if written == True: det.appendChild(off) center = doc.createElement("beam_center") written = write_node(doc, center, "x", item.beam_center.x, {"unit":item.beam_center_unit}) written = written | write_node(doc, center, "y", item.beam_center.y, {"unit":item.beam_center_unit}) written = written | write_node(doc, center, "z", item.beam_center.z, {"unit":item.beam_center_unit}) if written == True: det.appendChild(center) pix = doc.createElement("pixel_size") written = write_node(doc, pix, "x", item.pixel_size.x, {"unit":item.pixel_size_unit}) written = written | write_node(doc, pix, "y", item.pixel_size.y, {"unit":item.pixel_size_unit}) written = written | write_node(doc, pix, "z", item.pixel_size.z, {"unit":item.pixel_size_unit}) if written == True: det.appendChild(pix) ori = doc.createElement("orientation") written = write_node(doc, ori, "roll", item.orientation.x, {"unit":item.orientation_unit}) written = written | write_node(doc, ori, "pitch", item.orientation.y, {"unit":item.orientation_unit}) written = written | write_node(doc, ori, "yaw", item.orientation.z, {"unit":item.orientation_unit}) if written == True: det.appendChild(ori) # Processes info for item in datainfo.process: node = doc.createElement("SASprocess") entry_node.appendChild(node) write_node(doc, node, "name", item.name) write_node(doc, node, "date", item.date) write_node(doc, node, "description", item.description) for term in item.term: value = term['value'] del term['value'] write_node(doc, node, "term", value, term) for note in item.notes: write_node(doc, node, "SASprocessnote", note) # Return the document, and the SASentry node associated with # the data we just wrote return doc, entry_node def _parse_state(self, entry): """ Read a fit result from an XML node :param entry: XML node to read from :return: PageState object """ # Create an empty state state = None # Locate the P(r) node try: nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, namespaces={'ns': CANSAS_NS}) if nodes !=[]: # Create an empty state state = PageState() state.fromXML(node=nodes[0]) except: logging.info("XML document does not contain fitting information.\n %s" % sys.exc_value) return state def _parse_entry(self, dom): """ Parse a SASentry :param node: SASentry node :return: Data1D/Data2D object """ node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) if not node or node[0].text.lstrip().rstrip() != "Data2D": return CansasReader._parse_entry(self, dom) #Parse 2D data_info = Data2D() # Look up title self._store_content('ns:Title', dom, 'title', data_info) # Look up run number nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) for item in nodes: if item.text is not None: value = item.text.strip() if len(value) > 0: data_info.run.append(value) if item.get('name') is not None: data_info.run_name[value] = item.get('name') # Look up instrument name self._store_content('ns:SASinstrument/ns:name', dom, 'instrument', data_info) # Notes note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) for note in note_list: try: if note.text is not None: note_value = note.text.strip() if len(note_value) > 0: data_info.notes.append(note_value) except: err_mess = "cansas_reader.read: error processing entry notes\n %s" % sys.exc_value self.errors.append(err_mess) logging.error(err_mess) # Sample info ################### entry = get_content('ns:SASsample', dom) if entry is not None: data_info.sample.name = entry.get('name') self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample) self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', data_info.sample) self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', data_info.sample) self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', data_info.sample) nodes = dom.xpath('ns:SASsample/ns:details', namespaces={'ns': CANSAS_NS}) for item in nodes: try: if item.text is not None: detail_value = item.text.strip() if len(detail_value) > 0: data_info.sample.details.append(detail_value) except: err_mess = "cansas_reader.read: error processing sample details\n %s" % sys.exc_value self.errors.append(err_mess) logging.error(err_mess) # Position (as a vector) self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', data_info.sample) self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', data_info.sample) self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', data_info.sample) # Orientation (as a vector) self._store_float('ns:SASsample/ns:orientation/ns:roll', dom, 'orientation.x', data_info.sample) self._store_float('ns:SASsample/ns:orientation/ns:pitch', dom, 'orientation.y', data_info.sample) self._store_float('ns:SASsample/ns:orientation/ns:yaw', dom, 'orientation.z', data_info.sample) # Source info ################### entry = get_content('ns:SASinstrument/ns:SASsource', dom) if entry is not None: data_info.source.name = entry.get('name') self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', dom, 'radiation', data_info.source) self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', dom, 'beam_shape', data_info.source) self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', dom, 'wavelength', data_info.source) self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', dom, 'wavelength_min', data_info.source) self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', dom, 'wavelength_max', data_info.source) self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', dom, 'wavelength_spread', data_info.source) # Beam size (as a vector) entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) if entry is not None: data_info.source.beam_size_name = entry.get('name') self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', dom, 'beam_size.x', data_info.source) self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', dom, 'beam_size.y', data_info.source) self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', dom, 'beam_size.z', data_info.source) # Collimation info ################### nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', namespaces={'ns': CANSAS_NS}) for item in nodes: collim = Collimation() if item.get('name') is not None: collim.name = item.get('name') self._store_float('ns:length', item, 'length', collim) # Look for apertures apert_list = item.xpath('ns:aperture', namespaces={'ns': CANSAS_NS}) for apert in apert_list: aperture = Aperture() # Get the name and type of the aperture aperture.name = apert.get('name') aperture.type = apert.get('type') self._store_float('ns:distance', apert, 'distance', aperture) entry = get_content('ns:size', apert) if entry is not None: aperture.size_name = entry.get('name') self._store_float('ns:size/ns:x', apert, 'size.x', aperture) self._store_float('ns:size/ns:y', apert, 'size.y', aperture) self._store_float('ns:size/ns:z', apert, 'size.z', aperture) collim.aperture.append(aperture) data_info.collimation.append(collim) # Detector info ###################### nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', namespaces={'ns': CANSAS_NS}) for item in nodes: detector = Detector() self._store_content('ns:name', item, 'name', detector) self._store_float('ns:SDD', item, 'distance', detector) # Detector offset (as a vector) self._store_float('ns:offset/ns:x', item, 'offset.x', detector) self._store_float('ns:offset/ns:y', item, 'offset.y', detector) self._store_float('ns:offset/ns:z', item, 'offset.z', detector) # Detector orientation (as a vector) self._store_float('ns:orientation/ns:roll', item, 'orientation.x', detector) self._store_float('ns:orientation/ns:pitch', item, 'orientation.y', detector) self._store_float('ns:orientation/ns:yaw', item, 'orientation.z', detector) # Beam center (as a vector) self._store_float('ns:beam_center/ns:x', item, 'beam_center.x', detector) self._store_float('ns:beam_center/ns:y', item, 'beam_center.y', detector) self._store_float('ns:beam_center/ns:z', item, 'beam_center.z', detector) # Pixel size (as a vector) self._store_float('ns:pixel_size/ns:x', item, 'pixel_size.x', detector) self._store_float('ns:pixel_size/ns:y', item, 'pixel_size.y', detector) self._store_float('ns:pixel_size/ns:z', item, 'pixel_size.z', detector) self._store_float('ns:slit_length', item, 'slit_length', detector) data_info.detector.append(detector) # Processes info ###################### nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) for item in nodes: process = Process() self._store_content('ns:name', item, 'name', process) self._store_content('ns:date', item, 'date', process) self._store_content('ns:description', item, 'description', process) term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) for term in term_list: try: term_attr = {} for attr in term.keys(): term_attr[attr] = term.get(attr).strip() if term.text is not None: term_attr['value'] = term.text.strip() process.term.append(term_attr) except: err_mess = "cansas_reader.read: error processing process term\n %s" % sys.exc_value self.errors.append(err_mess) logging.error(err_mess) note_list = item.xpath('ns:SASprocessnote', namespaces={'ns': CANSAS_NS}) for note in note_list: if note.text is not None: process.notes.append(note.text.strip()) data_info.process.append(process) # Data info ###################### nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) if len(nodes)>1: raise RuntimeError, "CanSAS reader is not compatible with multiple SASdata entries" for entry in nodes: for item in list_of_data_2d_attr: #get node node = get_content('ns:%s'%item[0], entry) exec "data_info.%s = parse_entry_helper(node, item)"%(item[1]) for item in list_of_data2d_values: field = get_content('ns:%s'%item[0], entry) list = [] if field is not None: list = [parse_entry_helper(node, item) for node in field] exec "data_info.%s = numpy.array(list)"%item[0] return data_info def _read_cansas(self, path): """ Load data and P(r) 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 = [] basename = os.path.basename(path) root, extension = os.path.splitext(basename) ext = extension.lower() try: if os.path.isfile(path): #TODO: eventually remove the check for .xml once # the P(r) writer/reader is truly complete. if ext in self.ext or \ ext == '.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:SASentry', namespaces={'ns': CANSAS_NS}) for entry in entry_list: try: sas_entry = self._parse_entry(entry) except: raise fitstate = self._parse_state(entry) #state could be None when .svs file is loaded #in this case, skip appending to output if fitstate != None: sas_entry.meta_data['fitstate'] = fitstate sas_entry.filename = fitstate.file output.append(sas_entry) else: self.call_back(format=ext) raise RuntimeError, "%s is not a file" % path # Return output consistent with the loader's api if len(output)==0: self.call_back(state=None, datainfo=None,format=ext) return None else: for ind in range(len(output)): # Call back to post the new state state = output[ind].meta_data['fitstate'] t = time.localtime(state.timestamp) time_str = time.strftime("%b %d %H:%M", t) # Check that no time stamp is already appended max_char = state.file.find("[") if max_char < 0: max_char = len(state.file) original_fname = state.file[0:max_char] state.file = original_fname +' [' + time_str + ']' if state is not None and state.is_data is not None: exec 'output[%d].is_data = state.is_data'% ind output[ind].filename = state.file state.data = output[ind] state.data.name = output[ind].filename #state.data_name state.data.id = state.data_id if state.is_data is not None: state.data.is_data = state.is_data if output[ind].run_name is not None and len(output[ind].run_name) != 0 : name = output[ind].run_name else: name=original_fname state.data.group_id = name #store state in fitting self.call_back(state=state, datainfo=output[ind],format=ext) self.state= state return output except: self.call_back(format=ext) #self.state= state raise def write(self, filename, datainfo=None, fitstate=None): """ Write the content of a Data1D as a CanSAS XML file only for standalone :param filename: name of the file to write :param datainfo: Data1D object :param fitstate: PageState object """ # Sanity check if self.cansas == True: # Add fitting information to the XML document doc = self.write_toXML(datainfo, fitstate) # Write the XML document fd = open(filename, 'w') fd.write(doc.toprettyxml()) fd.close() else: fitstate.toXML(file=filename) def write_toXML(self, datainfo=None, state=None): """ Write toXML, a helper for write() , could be used by guimanager._on_save() : return: xml doc """ if state.data is None: data = sans.dataloader.data_info.Data1D(x=[], y=[]) else: #make sure title and data run is filled up. if state.data.title == None or state.data.title=='': state.data.title = state.data.name if state.data.run_name == None or state.data.run_name=={}: state.data.run = [str(state.data.name)] state.data.run_name[0] = state.data.name if issubclass(state.data.__class__, sans.dataloader.data_info.Data1D): data = state.data doc, sasentry = self._to_xml_doc(data) else: data = state.data doc, sasentry = self._data2d_to_xml_doc(data) if state is not None: state.toXML(doc=doc, file=data.name, entry_node=sasentry) return doc # Simple html report templet HEADER = "\n" HEADER += "\n" HEADER += " \n" HEADER += "\n" HEADER += "\n" HEADER += "\n" HEADER += "
\n" HEADER += "

" HEADER += "%s

" HEADER += "

 

" PARA = "

%s \n" PARA += "

" CENTRE = "

%s \n" CENTRE += "

" FEET_1 = \ """

 

Graph

 


Model Computation

Data: "%s"
""" FEET_2 = \ """ """ FEET_3 = \ """
""" ELINE = "

 

" if __name__ == "__main__": state = PageState(parent=None) #state.toXML() """ file = open("test_state", "w") pickle.dump(state, file) print pickle.dumps(state) state.data_name = "hello---->" pickle.dump(state, file) file = open("test_state", "r") new_state= pickle.load(file) print "new state", new_state new_state= pickle.load(file) print "new state", new_state #print "state", state """ import bsddb import pickle db= bsddb.btopen('file_state.db', 'c') val = (pickle.dumps(state), "hello", "hi") db['state1']= pickle.dumps(val) print pickle.loads(db['state1']) state.data_name = "hello---->22" db['state2']= pickle.dumps(state) state.data_name = "hello---->2" db['state3']= pickle.dumps(state) del db['state3'] state.data_name = "hello---->3" db['state4']= pickle.dumps(state) new_state = pickle.loads(db['state1']) #print db.last() db.set_location('state2') state.data_name = "hello---->5" db['aastate5']= pickle.dumps(state) db.keys().sort() print pickle.loads(db['state2']) db.close()