-#!/usr/bin/env python
-
-'''
-export.py
-
-Export commands for Hooke.
-
-Copyright 2010 by Dr. Rolf Schmidt (Concordia University, Canada)
-
-This program is released under the GNU General Public License version 2.
-'''
-
-import lib.libhooke as lh
-import wxversion
-wxversion.select(lh.WX_GOOD)
-
-import copy
-import os.path
-import time
-import wx
-
-class exportCommands(object):
- '''
- Export force curves, fits and results in different formats
- '''
-
- def _plug_init(self):
- pass
-
- def do_fits(self):
- '''
- Exports all fitting results (if available) in a columnar ASCII format.
- '''
- ext = self.GetStringFromConfig('export', 'fits', 'ext')
- folder = self.GetStringFromConfig('export', 'fits', 'folder')
- prefix = self.GetStringFromConfig('export', 'fits', 'prefix')
- separator = self.GetStringFromConfig('export', 'fits', 'separator')
- #TODO: add list for Tab, Space, Comma, Other
- #add string for Other
-
- active_file = self.GetActiveFile()
- plot = self.GetDisplayedPlot()
-
- #add empty columns before adding new results if necessary
- if plot is not None:
- for results_str, results in plot.results.items():
- for curve in results.results:
- output = []
- header_str = ''
- if curve.visible:
- header_str += curve.label + '_x (' + curve.units.x + ')' + separator + curve.label + '_y (' + curve.units.y + ')'
- output.append(header_str)
- for index, row in enumerate(curve.x):
- output.append(separator.join([str(curve.x[index]), str(curve.y[index])]))
- if output:
- #TODO: add option to replace or add the new file extension
- #add option to rename file from default.000 to default_000
- filename = os.path.basename(active_file.filename)
- filename = ''.join([prefix, filename, '_', curve.label, '.', ext])
- filename = os.path.join(folder, filename)
- output_file = open(filename, 'w')
- output_file.write('\n'.join(output))
- output_file.close
-
- def do_force_curve(self):
- '''
- TXT
- Saves the current curve as a text file
- Columns are, in order:
- X1 , Y1 , X2 , Y2 , X3 , Y3 ...
-
- -------------
- Syntax: txt [filename] {plot to export}
- '''
-
- ext = self.GetStringFromConfig('export', 'force_curve', 'ext')
- folder = self.GetStringFromConfig('export', 'force_curve', 'folder')
- prefix = self.GetStringFromConfig('export', 'force_curve', 'prefix')
- separator = self.GetStringFromConfig('export', 'force_curve', 'separator')
- #TODO: add list for Tab, Space, Comma, Other
- #add string for Other
-
- active_file = self.GetActiveFile()
- #create the header from the raw plot (i.e. only the force curve)
- plot = self.GetDisplayedPlotRaw()
-
- output = []
- header_str = ''
- for index, curve in enumerate(plot.curves):
- #TODO: only add labels for original curves (i.e. excluding anything added after the fact)
- header_str += curve.label + '_x (' + curve.units.x + ')' + separator + curve.label + '_y (' + curve.units.y + ')'
- if index < len(plot.curves) - 1:
- header_str += separator
- output.append(header_str)
-
- #export the displayed plot
- plot = self.GetDisplayedPlot()
- extension = plot.curves[lh.EXTENSION]
- retraction = plot.curves[lh.RETRACTION]
- for index, row in enumerate(extension.x):
- output.append(separator.join([str(extension.x[index]), str(extension.y[index]), str(retraction.x[index]), str(retraction.y[index])]))
-
- if output:
- #TODO: add option to replace or add the new file extension
- #add option to rename file from default.000 to default_000
- filename = os.path.basename(active_file.filename)
- filename = ''.join([prefix, filename, '.', ext])
- filename = os.path.join(folder, filename)
- output_file = open(filename, 'w')
- output_file.write('\n'.join(output))
- output_file.close
-
- def do_notes(self):
- '''
- Exports the note for all the files in a playlist.
- '''
- filename = self.GetStringFromConfig('export', 'notes', 'filename')
- folder = self.GetStringFromConfig('export', 'notes', 'folder')
- prefix = self.GetStringFromConfig('export', 'notes', 'prefix')
- use_playlist_filename = self.GetBoolFromConfig('export', 'notes', 'use_playlist_filename')
-
- playlist = self.GetActivePlaylist()
- output_str = ''
- for current_file in playlist.files:
- output_str = ''.join([output_str, current_file.filename, ' | ', current_file.note, '\n'])
- if output_str:
- output_str = ''.join(['Notes taken at ', time.asctime(), '\n', playlist.filename, '\n', output_str])
- if use_playlist_filename:
- path, filename = os.path.split(playlist.filename)
- filename = lh.remove_extension(filename)
- filename = ''.join([prefix, filename, '.txt'])
- filename = os.path.join(folder, filename)
- output_file = open(filename, 'w')
- output_file.write(output_str)
- output_file.close
- else:
- dialog = wx.MessageDialog(None, 'No notes found, file not saved.', 'Info', wx.OK)
- dialog.ShowModal()
-
- def do_overlay(self):
- '''
- Exports all retraction files in a playlist with the same scale.
- The files can then be overlaid in a graphing program to see which
- ones have the same shape.
- Use this export command only on filtered lists as it takes a long time
- to complete even with a small number of curves.
- '''
- playlist = self.GetActivePlaylist()
-
- filename_prefix = self.GetStringFromConfig('export', 'overlay', 'prefix')
-
- differences_x = []
- differences_y = []
- number_of_curves = playlist.count
- message_str = ''.join([str(number_of_curves), ' files to load.\n\n'])
- progress_dialog = wx.ProgressDialog('Loading', message_str, maximum=number_of_curves, parent=self, style=wx.PD_APP_MODAL|wx.PD_SMOOTH|wx.PD_AUTO_HIDE)
- for index, current_file in enumerate(playlist.files):
- current_file.identify(self.drivers)
- plot = current_file.plot
-
- plot.raw_curves = copy.deepcopy(plot.curves)
- #apply all active plotmanipulators and add the 'manipulated' data
- for plotmanipulator in self.plotmanipulators:
- if self.GetBoolFromConfig('core', 'plotmanipulators', plotmanipulator.name):
- plot = plotmanipulator.method(plot, current_file)
- #add corrected curves to plot
- plot.corrected_curves = copy.deepcopy(plot.curves)
-
- curve = current_file.plot.corrected_curves[lh.RETRACTION]
- differences_x.append(curve.x[0] - curve.x[-1])
- differences_y.append(curve.x[0] - curve.y[-1])
- progress_dialog.Update(index, ''.join([message_str, 'Loading ', str(index + 1), '/', str(number_of_curves)]))
- progress_dialog.Destroy()
-
- max_x = max(differences_x)
- max_y = max(differences_y)
- message_str = ''.join([str(number_of_curves), ' files to export.\n\n'])
- for index, current_file in enumerate(playlist.files):
- curve = current_file.plot.corrected_curves[lh.RETRACTION]
- first_x = curve.x[0]
- first_y = curve.y[0]
- new_x = [x - first_x for x in curve.x]
- new_y = [y - first_y for y in curve.y]
- new_x.append(-max_x)
- new_y.append(-max_y)
- output_str = ''
- for row_index, row in enumerate(new_x):
- output_str += ''.join([str(new_x[row_index]), ', ', str(new_y[row_index]), '\n'])
-
- if output_str:
- filename = ''.join([filename_prefix, current_file.name])
- filename = current_file.filename.replace(current_file.name, filename)
- output_file = open(filename, 'w')
- output_file.write(output_str)
- output_file.close
- progress_dialog.Destroy()
-
- def do_results(self, append=None, filename='', separator=''):
- '''
- Exports all visible fit results in a playlist into a delimited text file
- append: set append to True if you want to append to an existing results file
- filename: the filename and path of the results file
- separator: the separator between columns
- '''
- if not append:
- append = self.GetStringFromConfig('export', 'results', 'append')
- if filename == '':
- filename = self.GetStringFromConfig('export', 'results', 'filename')
- if separator == '':
- separator = self.GetStringFromConfig('export', 'results', 'separator')
-
- playlist = self.GetActivePlaylist()
- output_str = ''
- header_str = ''
- for current_file in playlist.files:
- if len(current_file.plot.results) > 0:
- for key in current_file.plot.results.keys():
- #if there are different types of fit results in the playlist, the header might have to change
- #here, we generate a temporary header and compare it to the current header
- #if they are different, the tempeorary header is used
- #we get the header from the fit and add the 'filename' column
- temporary_header_str = ''.join([current_file.plot.results[key].get_header_as_str(), separator, 'Filename'])
- if temporary_header_str != header_str:
- header_str = ''.join([current_file.plot.results[key].get_header_as_str(), separator, 'Filename'])
- output_str = ''.join([output_str, header_str, '\n'])
- for index, result in enumerate(current_file.plot.results[key].results):
- if result.visible:
- #similar to above, we get the result from the fit and add the filename
- line_str = current_file.plot.results[key].get_result_as_string(index)
- line_str = ''.join([line_str, separator, current_file.filename])
- output_str = ''.join([output_str, line_str, '\n'])
- if output_str:
- output_str = ''.join(['Analysis started ', time.asctime(), '\n', output_str])
-
- if append and os.path.isfile(filename):
- output_file = open(filename,'a')
- else:
- output_file = open(filename, 'w')
- output_file.write(output_str)
- output_file.close
- else:
- dialog = wx.MessageDialog(None, 'No results found, file not saved.', 'Info', wx.OK)
- dialog.ShowModal()
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