Source code for sas.sasgui.perspectives.file_converter.converter_panel

"""
This module provides a GUI for the file converter
"""

import wx
import sys
import os
import numpy as np
from wx.lib.scrolledpanel import ScrolledPanel
from sas.sasgui.guiframe.panel_base import PanelBase
from sas.sasgui.perspectives.calculator import calculator_widgets as widget
from sas.sasgui.perspectives.file_converter.converter_widgets import FileInput
from sas.sasgui.perspectives.file_converter.meta_panels import MetadataWindow
from sas.sasgui.perspectives.file_converter.meta_panels import DetectorPanel
from sas.sasgui.perspectives.file_converter.meta_panels import SamplePanel
from sas.sasgui.perspectives.file_converter.meta_panels import SourcePanel
from sas.sasgui.perspectives.file_converter.frame_select_dialog import FrameSelectDialog
from sas.sasgui.guiframe.events import StatusEvent
from sas.sasgui.guiframe.documentation_window import DocumentationWindow
from sas.sasgui.guiframe.dataFitting import Data1D
from sas.sascalc.dataloader.data_info import Data2D
from sas.sasgui.guiframe.utils import check_float
from sas.sascalc.file_converter.cansas_writer import CansasWriter
from sas.sascalc.file_converter.otoko_loader import OTOKOLoader
from sas.sascalc.file_converter.bsl_loader import BSLLoader
from sas.sascalc.file_converter.nxcansas_writer import NXcanSASWriter
from sas.sascalc.dataloader.data_info import Detector
from sas.sascalc.dataloader.data_info import Sample
from sas.sascalc.dataloader.data_info import Source
from sas.sascalc.dataloader.data_info import Vector

# Panel size
if sys.platform.count("win32") > 0:
    PANEL_TOP = 0
    _STATICBOX_WIDTH = 410
    _BOX_WIDTH = 200
    PANEL_SIZE = 480
    FONT_VARIANT = 0
else:
    PANEL_TOP = 60
    _STATICBOX_WIDTH = 430
    _BOX_WIDTH = 200
    PANEL_SIZE = 500
    FONT_VARIANT = 1

[docs]class ConverterPanel(ScrolledPanel, PanelBase): """ This class provides the File Converter GUI """ def __init__(self, parent, base=None, *args, **kwargs): ScrolledPanel.__init__(self, parent, *args, **kwargs) PanelBase.__init__(self) self.SetupScrolling() self.SetWindowVariant(variant=FONT_VARIANT) self.base = base self.parent = parent self.meta_frames = [] # GUI inputs self.q_input = None self.iq_input = None self.output = None self.radiation_input = None self.convert_btn = None self.metadata_section = None self.data_type = "ascii" # Metadata values self.title = '' self.run = '' self.run_name = '' self.instrument = '' self.detector = Detector() self.sample = Sample() self.source = Source() self.properties = ['title', 'run', 'run_name', 'instrument'] self.detector.name = '' self.source.radiation = 'neutron' self._do_layout() self.SetAutoLayout(True) self.Layout()
[docs] def convert_to_cansas(self, frame_data, filepath, single_file): """ Saves an array of Data1D objects to a single CanSAS file with multiple <SasData> elements, or to multiple CanSAS files, each with one <SasData> element. :param frame_data: If single_file is true, an array of Data1D objects. If single_file is false, a dictionary of the form frame_number: Data1D. :param filepath: Where to save the CanSAS file :param single_file: If true, array is saved as a single file, if false, each item in the array is saved to it's own file """ writer = CansasWriter() entry_attrs = None if self.run_name != '': entry_attrs = { 'name': self.run_name } if single_file: writer.write(filepath, frame_data, sasentry_attrs=entry_attrs) else: # Folder and base filename [group_path, group_name] = os.path.split(filepath) ext = "." + group_name.split('.')[-1] # File extension for frame_number, frame_data in frame_data.iteritems(): # Append frame number to base filename filename = group_name.replace(ext, str(frame_number)+ext) destination = os.path.join(group_path, filename) writer.write(destination, [frame_data], sasentry_attrs=entry_attrs)
[docs] def extract_ascii_data(self, filename): """ Extracts data from a single-column ASCII file :param filename: The file to load data from :return: A numpy array containing the extracted data """ try: data = np.loadtxt(filename, dtype=str) except: is_bsl = False # Check if file is a BSL or OTOKO header file f = open(filename, 'r') f.readline() f.readline() bsl_metadata = f.readline().strip().split() f.close() if len(bsl_metadata) == 10: msg = ("Error parsing ASII data. {} looks like a BSL or OTOKO " "header file.") raise Exception(msg.format(os.path.split(filename)[-1])) if len(data.shape) != 1: msg = "Error reading {}: Only one column of data is allowed" raise Exception(msg.format(filename.split('\\')[-1])) is_float = True try: float(data[0]) except: is_float = False if not is_float: end_char = data[0][-1] # If lines end with comma or semi-colon, trim the last character if end_char == ',' or end_char == ';': data = map(lambda s: s[0:-1], data) else: msg = ("Error reading {}: Lines must end with a digit, comma " "or semi-colon").format(filename.split('\\')[-1]) raise Exception(msg) return np.array(data, dtype=np.float32)
[docs] def extract_otoko_data(self, filename): """ Extracts data from a 1D OTOKO file :param filename: The OTOKO file to load the data from :return: A numpy array containing the extracted data """ loader = OTOKOLoader(self.q_input.GetPath(), self.iq_input.GetPath()) otoko_data = loader.load_otoko_data() qdata = otoko_data.q_axis.data iqdata = otoko_data.data_axis.data if len(qdata) > 1: msg = ("Q-Axis file has multiple frames. Only 1 frame is " "allowed for the Q-Axis") wx.PostEvent(self.parent.manager.parent, StatusEvent(status=msg, info="error")) return else: qdata = qdata[0] return qdata, iqdata
[docs] def extract_bsl_data(self, filename): """ Extracts data from a 2D BSL file :param filename: The header file to extract the data from :return x_data: A 1D array containing all the x coordinates of the data :return y_data: A 1D array containing all the y coordinates of the data :return frame_data: A dictionary of the form frame_number: data, where data is a 2D numpy array containing the intensity data """ loader = BSLLoader(filename) frames = [0] should_continue = True if loader.n_frames > 1: params = self.ask_frame_range(loader.n_frames) frames = params['frames'] if len(frames) == 0: should_continue = False elif loader.n_rasters == 1 and loader.n_frames == 1: message = ("The selected file is an OTOKO file. Please select the " "'OTOKO 1D' option if you wish to convert it.") dlg = wx.MessageDialog(self, message, 'Error!', wx.OK | wx.ICON_WARNING) dlg.ShowModal() should_continue = False dlg.Destroy() else: message = ("The selected data file only has 1 frame, it might be" " a multi-frame OTOKO file.\nContinue conversion?") dlg = wx.MessageDialog(self, message, 'Warning!', wx.YES_NO | wx.ICON_WARNING) should_continue = (dlg.ShowModal() == wx.ID_YES) dlg.Destroy() if not should_continue: return None frame_data = loader.load_frames(frames) return frame_data
[docs] def ask_frame_range(self, n_frames): """ Display a dialog asking the user to input the range of frames they would like to export :param n_frames: How many frames the loaded data file has :return: A dictionary containing the parameters input by the user """ valid_input = False _, ext = os.path.splitext(self.output.GetPath()) show_single_btn = (ext == '.h5') dlg = FrameSelectDialog(n_frames, show_single_btn) frames = None increment = None single_file = True while not valid_input: if dlg.ShowModal() == wx.ID_OK: msg = "" try: first_frame = int(dlg.first_input.GetValue()) last_frame = int(dlg.last_input.GetValue()) increment = int(dlg.increment_input.GetValue()) if not show_single_btn: single_file = dlg.single_btn.GetValue() if last_frame < 0 or first_frame < 0: msg = "Frame values must be positive" elif increment < 1: msg = "Increment must be greater than or equal to 1" elif first_frame > last_frame: msg = "First frame must be less than last frame" elif last_frame >= n_frames: msg = "Last frame must be less than {}".format(n_frames) else: valid_input = True except: valid_input = False msg = "Please enter valid integer values" if not valid_input: wx.PostEvent(self.parent.manager.parent, StatusEvent(status=msg)) else: return { 'frames': [], 'inc': None, 'file': single_file } frames = range(first_frame, last_frame + 1, increment) return { 'frames': frames, 'inc': increment, 'file': single_file }
[docs] def get_metadata(self): # Prepare the metadata for writing to a file if self.run is None: self.run = [] elif not isinstance(self.run, list): self.run = [self.run] run_name = None if len(self.run) > 0: run_number = self.run[0] run_name = { run_number: self.run_name } if self.title is None: self.title = '' metadata = { 'title': self.title, 'run': self.run, 'run_name': run_name, 'instrument': self.instrument, 'detector': [self.detector], 'sample': self.sample, 'source': self.source } return metadata
[docs] def convert_1d_data(self, qdata, iqdata): """ Formats a 1D array of q_axis data and a 2D array of I axis data (where each row of iqdata is a separate row), into an array of Data1D objects """ frames = [] increment = 1 single_file = True n_frames = iqdata.shape[0] # Standard file has 3 frames: SAS, calibration and WAS if n_frames > 3: # File has multiple frames - ask the user which ones they want to # export params = self.ask_frame_range(n_frames) frames = params['frames'] increment = params['inc'] single_file = params['file'] if frames == []: return else: # Only interested in SAS data frames = [0] output_path = self.output.GetPath() metadata = self.get_metadata() frame_data = {} for i in frames: data = Data1D(x=qdata, y=iqdata[i]) frame_data[i] = data if single_file: # Only need to set metadata on first Data1D object frame_data = frame_data.values() # Don't need to know frame numbers frame_data[0].filename = output_path.split('\\')[-1] for key, value in metadata.iteritems(): setattr(frame_data[0], key, value) else: # Need to set metadata for all Data1D objects for datainfo in frame_data.values(): datainfo.filename = output_path.split('\\')[-1] for key, value in metadata.iteritems(): setattr(datainfo, key, value) _, ext = os.path.splitext(output_path) if ext == '.xml': self.convert_to_cansas(frame_data, output_path, single_file) else: # ext == '.h5' w = NXcanSASWriter() w.write(frame_data, output_path)
[docs] def on_convert(self, event): """Called when the Convert button is clicked""" if not self.validate_inputs(): return self.sample.ID = self.title try: if self.data_type == 'ascii': qdata = self.extract_ascii_data(self.q_input.GetPath()) iqdata = np.array([self.extract_ascii_data(self.iq_input.GetPath())]) self.convert_1d_data(qdata, iqdata) elif self.data_type == 'otoko': qdata, iqdata = self.extract_otoko_data(self.q_input.GetPath()) self.convert_1d_data(qdata, iqdata) else: # self.data_type == 'bsl' dataset = self.extract_bsl_data(self.iq_input.GetPath()) if dataset is None: # Cancelled by user return metadata = self.get_metadata() for key, value in metadata.iteritems(): setattr(dataset[0], key, value) w = NXcanSASWriter() w.write(dataset, self.output.GetPath()) except Exception as ex: msg = str(ex) wx.PostEvent(self.parent.manager.parent, StatusEvent(status=msg, info='error')) return wx.PostEvent(self.parent.manager.parent, StatusEvent(status="Conversion completed."))
[docs] def on_help(self, event): """ Show the File Converter documentation """ tree_location = ("user/sasgui/perspectives/file_converter/" "file_converter_help.html") doc_viewer = DocumentationWindow(self, -1, tree_location, "", "File Converter Help")
[docs] def validate_inputs(self): msg = "You must select a" if self.q_input.GetPath() == '' and self.data_type != 'bsl': msg += " Q Axis input file." elif self.iq_input.GetPath() == '': msg += "n Intensity input file." elif self.output.GetPath() == '': msg += " destination for the converted file." if msg != "You must select a": wx.PostEvent(self.parent.manager.parent, StatusEvent(status=msg, info='error')) return return True
[docs] def show_detector_window(self, event): """ Show the window for inputting Detector metadata """ if self.meta_frames != []: for frame in self.meta_frames: frame.panel.on_close() detector_frame = MetadataWindow(DetectorPanel, parent=self.parent.manager.parent, manager=self, metadata=self.detector, title='Detector Metadata') self.meta_frames.append(detector_frame) self.parent.manager.put_icon(detector_frame) detector_frame.Show(True)
[docs] def show_sample_window(self, event): """ Show the window for inputting Sample metadata """ if self.meta_frames != []: for frame in self.meta_frames: frame.panel.on_close() sample_frame = MetadataWindow(SamplePanel, parent=self.parent.manager.parent, manager=self, metadata=self.sample, title='Sample Metadata') self.meta_frames.append(sample_frame) self.parent.manager.put_icon(sample_frame) sample_frame.Show(True)
[docs] def show_source_window(self, event): """ Show the window for inputting Source metadata """ if self.meta_frames != []: for frame in self.meta_frames: frame.panel.on_close() source_frame = MetadataWindow(SourcePanel, parent=self.parent.manager.parent, manager=self, metadata=self.source, title="Source Metadata") self.meta_frames.append(source_frame) self.parent.manager.put_icon(source_frame) source_frame.Show(True)
[docs] def on_collapsible_pane(self, event): """ Resize the scrollable area to fit the metadata pane when it's collapsed or expanded """ self.Freeze() self.SetupScrolling() self.parent.Layout() self.Thaw()
[docs] def datatype_changed(self, event): """ Update the UI and self.data_type when a data type radio button is pressed """ event.Skip() dtype = event.GetEventObject().GetName() self.data_type = dtype if dtype == 'bsl': self.q_input.SetPath("") self.q_input.Disable() self.output.SetWildcard("NXcanSAS HDF5 File (*.h5)|*.h5") else: self.q_input.Enable() self.radiation_input.Enable() self.metadata_section.Enable() self.output.SetWildcard("CanSAS 1D (*.xml)|*.xml|NXcanSAS HDF5 File (*.h5)|*.h5")
[docs] def radiationtype_changed(self, event): event.Skip() rtype = event.GetEventObject().GetValue().lower() self.source.radiation = rtype
[docs] def metadata_changed(self, event): event.Skip() textbox = event.GetEventObject() attr = textbox.GetName() value = textbox.GetValue().strip() setattr(self, attr, value)
def _do_layout(self): vbox = wx.BoxSizer(wx.VERTICAL) instructions = ( "Select linked single column 1D ASCII files containing the Q-axis and " "Intensity-axis data, or 1D BSL/OTOKO files, or a 2D BSL/OTOKO file, " "then choose where to save the converted file, and click Convert.\n" "1D ASCII and BSL/OTOKO files can be converted to CanSAS (XML) or " "NXcanSAS (HDF5) formats. 2D BSL/OTOKO files can only be converted to " "the NXcanSAS format.\n" "Metadata can be optionally added for the CanSAS XML format." ) instruction_label = wx.StaticText(self, -1, instructions, size=(_STATICBOX_WIDTH+40, -1)) instruction_label.Wrap(_STATICBOX_WIDTH+40) vbox.Add(instruction_label, flag=wx.TOP | wx.LEFT | wx.RIGHT, border=5) section = wx.StaticBox(self, -1) section_sizer = wx.StaticBoxSizer(section, wx.VERTICAL) section_sizer.SetMinSize((_STATICBOX_WIDTH, -1)) input_grid = wx.GridBagSizer(5, 5) y = 0 data_type_label = wx.StaticText(self, -1, "Input Format: ") input_grid.Add(data_type_label, (y,0), (1,1), wx.ALIGN_CENTER_VERTICAL, 5) radio_sizer = wx.BoxSizer(wx.HORIZONTAL) ascii_btn = wx.RadioButton(self, -1, "ASCII", name="ascii", style=wx.RB_GROUP) ascii_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed) radio_sizer.Add(ascii_btn) otoko_btn = wx.RadioButton(self, -1, "BSL 1D", name="otoko") otoko_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed) radio_sizer.Add(otoko_btn) input_grid.Add(radio_sizer, (y,1), (1,1), wx.ALL, 5) bsl_btn = wx.RadioButton(self, -1, "BSL 2D", name="bsl") bsl_btn.Bind(wx.EVT_RADIOBUTTON, self.datatype_changed) radio_sizer.Add(bsl_btn) y += 1 q_label = wx.StaticText(self, -1, "Q-Axis Data: ") input_grid.Add(q_label, (y,0), (1,1), wx.ALIGN_CENTER_VERTICAL, 5) self.q_input = wx.FilePickerCtrl(self, -1, size=(_STATICBOX_WIDTH-80, -1), message="Chose the Q-Axis data file.", style=wx.FLP_USE_TEXTCTRL | wx.FLP_CHANGE_DIR) input_grid.Add(self.q_input, (y,1), (1,1), wx.ALL, 5) y += 1 iq_label = wx.StaticText(self, -1, "Intensity-Axis Data: ") input_grid.Add(iq_label, (y,0), (1,1), wx.ALIGN_CENTER_VERTICAL, 5) self.iq_input = wx.FilePickerCtrl(self, -1, size=(_STATICBOX_WIDTH-80, -1), message="Chose the Intensity-Axis data file.", style=wx.FLP_USE_TEXTCTRL | wx.FLP_CHANGE_DIR) input_grid.Add(self.iq_input, (y,1), (1,1), wx.ALL, 5) y += 1 radiation_label = wx.StaticText(self, -1, "Radiation Type: ") input_grid.Add(radiation_label, (y,0), (1,1), wx.ALIGN_CENTER_VERTICAL, 5) self.radiation_input = wx.ComboBox(self, -1, choices=["Neutron", "X-Ray", "Muon", "Electron"], name="radiation", style=wx.CB_READONLY, value="Neutron") self.radiation_input.Bind(wx.EVT_COMBOBOX, self.radiationtype_changed) input_grid.Add(self.radiation_input, (y,1), (1,1), wx.ALL, 5) y += 1 output_label = wx.StaticText(self, -1, "Output File: ") input_grid.Add(output_label, (y,0), (1,1), wx.ALIGN_CENTER_VERTICAL, 5) self.output = FileInput(self, wildcard="CanSAS 1D (*.xml)|*.xml|NXcanSAS HDF5 File (*.h5)|*.h5") input_grid.Add(self.output.GetCtrl(), (y,1), (1,1), wx.EXPAND | wx.ALL, 5) y += 1 self.convert_btn = wx.Button(self, wx.ID_OK, "Stop Converstion") self.convert_btn.SetLabel("Convert") input_grid.Add(self.convert_btn, (y,0), (1,1), wx.ALL, 5) self.convert_btn.Bind(wx.EVT_BUTTON, self.on_convert) help_btn = wx.Button(self, -1, "HELP") input_grid.Add(help_btn, (y,1), (1,1), wx.ALL, 5) help_btn.Bind(wx.EVT_BUTTON, self.on_help) section_sizer.Add(input_grid) vbox.Add(section_sizer, flag=wx.ALL, border=5) self.metadata_section = wx.CollapsiblePane(self, -1, "Metadata", size=(_STATICBOX_WIDTH+40, -1), style=wx.WS_EX_VALIDATE_RECURSIVELY) metadata_pane = self.metadata_section.GetPane() metadata_grid = wx.GridBagSizer(5, 5) self.metadata_section.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.on_collapsible_pane) y = 0 for item in self.properties: # Capitalise each word label_txt = " ".join( [s.capitalize() for s in item.replace('_', ' ').split(' ')]) if item == 'run': label_txt = "Run Number" label = wx.StaticText(metadata_pane, -1, label_txt, style=wx.ALIGN_CENTER_VERTICAL) input_box = wx.TextCtrl(metadata_pane, name=item, size=(_STATICBOX_WIDTH-80, -1)) input_box.Bind(wx.EVT_TEXT, self.metadata_changed) metadata_grid.Add(label, (y,0), (1,1), wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5) metadata_grid.Add(input_box, (y,1), (1,2), wx.EXPAND) y += 1 detector_label = wx.StaticText(metadata_pane, -1, "Detector:") metadata_grid.Add(detector_label, (y, 0), (1,1), wx.ALL | wx.EXPAND, 5) detector_btn = wx.Button(metadata_pane, -1, "Enter Detector Metadata") metadata_grid.Add(detector_btn, (y, 1), (1,1), wx.ALL | wx.EXPAND, 5) detector_btn.Bind(wx.EVT_BUTTON, self.show_detector_window) y += 1 sample_label = wx.StaticText(metadata_pane, -1, "Sample: ") metadata_grid.Add(sample_label, (y,0), (1,1), wx.ALL | wx.EXPAND, 5) sample_btn = wx.Button(metadata_pane, -1, "Enter Sample Metadata") metadata_grid.Add(sample_btn, (y,1), (1,1), wx.ALL | wx.EXPAND, 5) sample_btn.Bind(wx.EVT_BUTTON, self.show_sample_window) y += 1 source_label = wx.StaticText(metadata_pane, -1, "Source: ") metadata_grid.Add(source_label, (y,0), (1,1), wx.ALL | wx.EXPAND, 5) source_btn = wx.Button(metadata_pane, -1, "Enter Source Metadata") source_btn.Bind(wx.EVT_BUTTON, self.show_source_window) metadata_grid.Add(source_btn, (y,1), (1,1), wx.ALL | wx.EXPAND, 5) y += 1 metadata_pane.SetSizer(metadata_grid) vbox.Add(self.metadata_section, proportion=0, flag=wx.ALL, border=5) vbox.Fit(self) self.SetSizer(vbox)
[docs]class ConverterWindow(widget.CHILD_FRAME): """Displays ConverterPanel""" def __init__(self, parent=None, title='File Converter', base=None, manager=None, size=(PANEL_SIZE * 1.05, PANEL_SIZE / 1.1), *args, **kwargs): kwargs['title'] = title kwargs['size'] = size widget.CHILD_FRAME.__init__(self, parent, *args, **kwargs) self.manager = manager self.panel = ConverterPanel(self, base=None) self.Bind(wx.EVT_CLOSE, self.on_close) self.SetPosition((wx.LEFT, PANEL_TOP)) self.Show(True)
[docs] def on_close(self, event): if self.manager is not None: self.manager.converter_frame = None self.Destroy()