"""
"""
#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 + "%" + 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 + "%" + 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 + "%" + 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('%', '%')
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