From 8eaf76629de225cf6752c7ab32653312f212631e Mon Sep 17 00:00:00 2001 From: Sylvain Tricot Date: Tue, 8 Dec 2020 21:29:30 +0100 Subject: [PATCH] start porting the code from WX to GTK3. --- src/msspec/iodata_gi.py | 1717 +++++++++++++++++++++++++++++++++++++++ src/msspec/iodata_wx.py | 1455 +++++++++++++++++++++++++++++++++ 2 files changed, 3172 insertions(+) create mode 100644 src/msspec/iodata_gi.py create mode 100644 src/msspec/iodata_wx.py diff --git a/src/msspec/iodata_gi.py b/src/msspec/iodata_gi.py new file mode 100644 index 0000000..4eb0e91 --- /dev/null +++ b/src/msspec/iodata_gi.py @@ -0,0 +1,1717 @@ +#!/usr/bin/env python +# +# Copyright © 2016-2020 - Rennes Physics Institute +# +# This file is part of msspec. +# +# msspec is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# msspec is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# You should have received a copy of the GNU General Public License +# along with this msspec. If not, see . +# +# Source file : src/msspec/iodata.py +# Last modified: ven. 10 avril 2020 17:23:11 +# Committed by : "Sylvain Tricot " + + +""" +Module iodata +============= + +This module contains all classes useful to manipulate, store and display +data results. + +The :py:class:`Data` and :py:class:`DataSet` are the two enduser classes +important to manipulate the data. +Here is an example of how to store values in a Data object: + +.. code-block:: python + + from msspec.iodata import Data + import numpy as np + + + # Let's create first some dumy data + X = np.arange(0, 20) + Y = X**2 + + # Create a Data object. You need to give a title as an argument + data = Data('all my data') + # and append a new DataSet with its title + dset = data.add_dset('Dataset 0') + + # To feed the DataSet with columns, use the add_columns method + # and provide as many keywords as you like. Each key being the + # column name and each value being an array holding the column + # data. + dset.add_columns(x=X, y=Y, z=X+2, w=Y**3) + # you can provide parameters with their values with keywords as well + dset.add_parameter(name='truc', group='main', value='3.14', unit='eV') + + # To plot these data, you need to add a 'view' with its title + view = dset.add_view('my view') + # You then need to select which columns you which to plot and + # and under wich conditions (with the 'which' keyword) + view.select('x', 'y', where="z<10", legend=r"z = 0") + view.select('x', 'y', where="z>10", legend=r"z = 1") + + # To pop up the graphical window + data.view() + +""" + + +import os +import sys +from distutils.version import LooseVersion +from distutils.version import StrictVersion +from io import StringIO +from datetime import datetime + +import ase.io +import h5py +import numpy as np +import wx.grid +from lxml import etree +from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvas +#from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas +#from matplotlib.backends.backend_wxagg import FigureCanvasWx as FigureCanvas +from matplotlib.backends.backend_agg import FigureCanvasAgg +from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg +from matplotlib.figure import Figure +from terminaltables import AsciiTable + +import msspec +from msspec.msspecgui.msspec.gui.clusterviewer import ClusterViewer +from msspec.misc import LOGGER + +import gi +gi.require_version("Gtk", "3.0") +from gi.repository import Gtk, Gio, GLib + + +MENU_XML = """ + + + + + File +
+ + app.open + _Open + <Primary>o + + + app.save + _Save + <Primary>s + + + app.saveas + Save as... + + + app.export + Export + <Primary>e + +
+
+ + win.quit + _Quit + <Primary>q + +
+ + + + Datasets + + + +""" + + + + + + + +def cols2matrix(x, y, z, nx=88*1+1, ny=360*1+1): + # mix the values of existing theta and new theta and return the + # unique values + newx = np.linspace(np.min(x), np.max(x), nx) + newy = np.linspace(np.min(y), np.max(y), ny) + ux = np.unique(np.append(x, newx)) + uy = np.unique(np.append(y, newy)) + + # create an empty matrix to hold the results + zz = np.empty((len(ux), len(uy))) + zz[:] = np.nan + + for p in zip(x, y, z): + i = np.argwhere(ux == p[0]) + j = np.argwhere(uy == p[1]) + zz[i, j] = p[2] + + for i in range(len(ux)): + #ok, = np.where(-np.isnan(zz[i,:])) + ok, = np.where(~np.isnan(zz[i, :])) + if len(ok) > 0: + xp = uy[ok] + fp = zz[i, ok] + zz[i,:] = np.interp(uy, xp, fp) + + for i in range(len(uy)): + #ok, = np.where(-np.isnan(zz[:,i])) + ok, = np.where(~np.isnan(zz[:, i])) + if len(ok) > 0: + xp = ux[ok] + fp = zz[ok, i] + zz[:,i] = np.interp(ux, xp, fp) + + return ux, uy, zz + + +def is_title_valid(title): + """ Ensure the string does not contain special characters: + /\:*?"<>| + """ + special_chars = ('/', '\\', ':', '*', '?', '\"', '<', '>', '|') + for char in special_chars: + if title.find(char) > -1: + return False + return True + + + +class _DataPoint(dict): + def __init__(self, *args, **kwargs): + dict.__init__(self, *args, **kwargs) + + def __getattr__(self, name): + if name in list(self.keys()): + return self[name] + else: + raise AttributeError("'{}' object has no attribute '{}'".format( + self.__class__.__name__, name)) + +class DataSet(object): + """ + This class can create an object to hold column-oriented data. + + :param title: The text used to entitled the dataset + :type title: str + :param notes: Some comments to add to the data + :type notes: str + + """ + def __init__(self, title, notes=""): + assert is_title_valid(title), '\/:*?"<>| are not allowed in the string' + #self._col_names = [] + #self._col_arrays = [] + self.__dict__['_col_names'] = [] + self.__dict__['_col_arrays'] = [] + + self.title = title + self.notes = notes + self._views = [] + self._parameters = [] + self.attributes = {} + + + self._defaults = {'bool': False, 'str': '', 'int': 0, 'float': 0., + 'complex': complex(0)} + self._formats = {bool: '{:s}', str: '{:s}', int: '{:<20d}', + float: '{:<20.10e}', complex: 's'} + self._formats = ((np.integer, '{:<20d}'), + (np.floating, '{:<20.10e}'), + (np.complex, '({0.real:<.10e} {0.imag:<.10e}j)'), + (np.bool, '{:s}'), + (str, '{:s}')) + + + def _empty_array(self, val): + if isinstance(val, str): + t = 'S256' + else: + t = np.dtype(type(val)) + + if isinstance(val, bool): + default = self._defaults['bool'] + elif isinstance(val, str): + default = self._defaults['str'] + elif isinstance(val, int): + default = self._defaults['int'] + elif isinstance(val, float): + default = self._defaults['float'] + elif isinstance(val, complex): + default = self._defaults['complex'] + else: + raise TypeError('Not a supported type') + + return np.array([default]*len(self), dtype=t) + + def add_row(self, **kwargs): + """Add a row of data into the dataset. + + :param kwargs: Each keyword is a column name. The number of keywords (columns) must be coherent with the + number of existing columns. If no column are defined yet, they will be created. + + """ + for k, v in list(kwargs.items()): + if k not in self._col_names: + self._col_names.append(k) + self._col_arrays.append(self._empty_array(v)) + for k, v in list(kwargs.items()): + i = self._col_names.index(k) + arr = self._col_arrays[i] + arr = np.append(arr, v) + self._col_arrays[i] = arr + + def add_columns(self, **kwargs): + """ + Add columns to the dataset. + + You can provide as many columns as you want to this function. This + function can be called several times on the same dataset but each time + with different column names. Column names are given as keywords. + + :Example: + + >>> from iodata import DataSet + >>> dset = DataSet('My Dataset', notes="Just an example") + >>> xdata = range(10) + >>> ydata = [i**2 for i in xdata] + >>> dset.add_columns(x=xdata, y=ydata) + >>> print dset + >>> +-------+ + >>> | x y | + >>> +-------+ + >>> | 0 0 | + >>> | 1 1 | + >>> | 2 4 | + >>> | 3 9 | + >>> | 4 16 | + >>> | 5 25 | + >>> | 6 36 | + >>> | 7 49 | + >>> | 8 64 | + >>> | 9 81 | + >>> +-------+ + + """ + for k, vv in list(kwargs.items()): + assert k not in self._col_names, ("'{}' column already exists" + "".format(k)) + #if len(self) > 0: + # assert len(vv) == len(self), ( + # 'Too many values in the column (max = {})'.format( + # len(self))) + for k, vv in list(kwargs.items()): + arr = np.array(vv) + self._col_names.append(k) + self._col_arrays.append(arr) + + def delete_rows(self, itemspec): + """ + Delete the rows specified with itemspec. + + """ + for i in range(len(self._col_names)): + self._col_arrays[i] = np.delete(self._col_arrays[i], itemspec) + + def delete_columns(self, *tags): + """ + Removes all columns name passed as arguments + + :param tags: column names. + :type tags: str + + """ + for tag in tags: + i = self._col_names.index(tag) + self._col_names.pop(i) + self._col_arrays.pop(i) + + def columns(self): + """ + Get all the column names. + + :return: List of column names. + :rtype: List of str + + """ + return self._col_names + + def add_view(self, name, overwrite=False, **plotopts): + """ + Creates a new view named *name* with specied plot options. + + :param name: name of the view. + :type name: str + :param plotopts: list of keywords for configuring the plots. + :return: a view. + :rtype: :py:class:`iodata._DataSetView` + """ + if overwrite: + self.delete_view(name) + + if isinstance(name, str): + v = _DataSetView(self, name, **plotopts) + else: + v = name + v.dataset = self + self._views.append(v) + return v + + def delete_view(self, name): + view_titles = [_.title for _ in self._views] + try: + i = view_titles.index(name) + self._views.pop(i) + except: + pass + + def views(self): + """Returns all the defined views in the dataset. + + :return: A list of view + :rtype: List of :py:class:`iodata._DataSetView` + """ + return self._views + + def add_parameter(self, **kwargs): + """Add a parameter to store with the dataset. + + :param kwargs: list of keywords with str values. + + These keywords are: + * name: the name of the parameter. + * group: the name of a group it belongs to. + * value: the value of the parameter. + * unit: the unit of the parameter. + + For example: + + .. code-block:: python + + from iodata import DataSet + + mydset = DataSet("Experiment") + mydset.add_parameter(name='Spectrometer', group='misc', value='Omicron', unit='') + + """ + self._parameters.append(kwargs) + + def parameters(self): + """ + Returns the list of defined parameters. + + :return: all parameters defined in the :py:class:`iodata.DataSet` object. + :rtype: List of dict + """ + return self._parameters + + def get_parameter(self, group=None, name=None): + """Retrieves all parameters for a given name and group. + + * If *name* is given and *group* is None, returns all parameters with such a *name* in all groups. + * If *group* is given and *name* is None, returns all parameters in such a *group* + * If both *name* and *group* are None. Returns all parameters (equivalent to + :py:func:`iodata.DataSet.parameters`). + + :param group: The group name or None. + :type group: str + :param name: The parameter's name or None. + :type name: str + :return: A list of parameters. + :rtype: List of dict + """ + p = [] + for _ in self._parameters: + if _['group'] == group or group == None: + if _['name'] == name or name == None: + p.append(_) + return p[0] if len(p) == 1 else p + + def get_cluster(self): + """Get all the atoms in the cluster. + + :return: The cluster + :rtype: :py:class:`ase.Atoms` + """ + s = StringIO() + s.write(self.get_parameter(group='Cluster', name='cluster')['value']) + return ase.io.read(s, format='xyz') + + + def select(self, *args, **kwargs): + condition = kwargs.get('where', 'True') + indices = [] + + def export_views(self, folder): + for view in self.views(): + f = view.get_figure() + fname = os.path.join(folder, view.title) + '.png' + f.savefig(fname) + + + def export(self, filename="", mode="w"): + """Export the DataSet to the given *filename*. + + :param filename: The name of the file. + :type filename: str + + .. warning:: + + Not yet implemented + """ + + rule = '#' * 80 + '\n' + + def header(): + s = '# PARAMETERS:\n' + groups = [] + for p in self.parameters(): + g = p['group'] + if g not in groups: + groups.append(g) + parameters = {} + for group in groups: + parameters[group] = self.get_parameter(group=group) + for k, v in parameters.items(): + if k == 'Cluster': + continue + s += f"# {k}:\n" + if not(isinstance(v, list)): + v = [v,] + for p in v: + s += f"# {p['name']} = {p['value']} {p['unit']}\n" + return s + + colnames = self.columns() + with open(filename, mode) as fd: + # write the date and time of export + now = datetime.now() + fd.write(f"# Data exported on {now}\n") + fd.write(rule) + + # Append notes + fd.write("# NOTES:\n") + for line in self.notes.split('\n'): + fd.write(f"# {line}\n") + fd.write(rule) + + # Append parameters + fd.write(header()) + fd.write(rule) + + # Append the data + fd.write("# DATA:\n") + fd.write("# " + ("{:<20s}" * len(colnames)).format(*colnames + ) + "\n") + for i in range(len(self)): + row = self[i] + for key in row.columns(): + value = row[key][0] + fmt = '{:s}' + #print value + for t, f in self._formats: + if isinstance(value, t): + fmt = f + break + #fd.write(' ') + fd.write(fmt.format(value)) + #fd.write(str(value) + ', ') + fd.write('\n') + + def __getitem__(self, itemspec): + if isinstance(itemspec, str): + return getattr(self, itemspec) + title = 'untitled' + new = DataSet(title) + + new._col_names = self.columns() + for arr in self._col_arrays: + new._col_arrays.append(np.asarray(arr)[itemspec].flatten()) + + return new + + def __setstate__(self, state): + self.__dict__ = state + + def __getstate__(self): + return self.__dict__ + + def __getattr__(self, name): + if name in self._col_names: + i = self._col_names.index(name) + return self._col_arrays[i] + else: + raise AttributeError("'{}' object has no attribute '{}'".format( + self.__class__.__name__, name)) + + def __setattr__(self, name, value): + if name in self._col_names: + i = self._col_names.index(name) + self._col_arrays[i] = value + else: + self.__dict__[name] = value + + def __iter__(self): + for i in range(len(self)): + _ = {k: arr[i] for k, arr in zip(self._col_names, + self._col_arrays)} + point = _DataPoint(_) + yield point + + def __len__(self): + try: + #length = len(self._col_arrays[0]) + length = 0 + for array in self._col_arrays: + length = max(length, len(array)) + except IndexError: + length = 0 + return length + + def __str__(self): + max_len = 10 + max_col = 10 + ncols = min(max_col, len(self._col_arrays)) + table_data = [self._col_names[:ncols]] + table_data[0].insert(0, "") + + all_indices = np.arange(0, len(self)) + indices = all_indices + if len(self) > max_len: + indices = list(range(int(max_len/2))) + list(range(int(-max_len/2), 0)) + + _i = 0 + for i in indices: + if i < _i: + row = ['...' for _ in range(ncols + 1)] + table_data.append(row) + row = [str(all_indices[i]),] + for j in range(ncols): + arr = self._col_arrays[j] + row.append(str(arr[i])) + if len(self._col_names) > max_col: + row.append('...') + table_data.append(row) + _i = i + + table = AsciiTable(table_data) + table.outer_border = True + table.title = self.title + table.inner_column_border = False + return table.table + + def __repr__(self): + s = "<{}('{}')>".format(self.__class__.__name__, self.title) + return s + +class Data(object): + """Creates a new Data object to store DataSets. + + :param title: The title of the Data object. + :type str: + + """ + def __init__(self, title=''): + assert is_title_valid(title), '\/:*?"<>| are not allowed in the string' + self.title = title + self._datasets = [] + self._dirty = False + + def add_dset(self, title, overwrite=False): + """Adds a new DataSet in the Data object. + + :param title: The name of the DataSet. + :type title: str + :param overwrite: Tells whether to re-create the dataset if it exists. + :type overwrite: bool + :return: The newly created DataSet. + :rtype: :py:class:`iodata.DataSet` + """ + if overwrite: + try: + self.delete_dset(title) + except Exception as err: + pass + + titles = [d.title for d in self._datasets] + if not title in titles: + dset = DataSet(title) + self._datasets.append(dset) + self._dirty = True + return dset + else: + raise NameError('A Dataset with that name already exists!') + + def delete_dset(self, title): + """Removes a DataSet from the Data object. + + :param title: The DataSet name to be removed. + :type title: str + + """ + titles = [d.title for d in self._datasets] + i = titles.index(title) + self._datasets.pop(i) + self._dirty = True + + def get_last_dset(self): + """Get the last DataSet of the Data object. + + :return: The lastly created DataSet in the Data object + :rtype: :py:class:`iodata.DataSet` + """ + return self._datasets[-1] + + def is_dirty(self): + """Wether the Data object needs to be saved. + + :return: A boolean value to indicate if Data has changed since last dump to hard drive. + :rtype: bool + """ + return self._dirty + + + def save(self, filename, append=False): + """Saves the current Data to the hard drive. + + The Data, all its content along with parameters, defined views... are saved to the hard drive in the HDF5 + file format. Please see `hdfgroup `_ for more details about HDF5. + + :param filename: The name of the file to create or to append to. + :type filename: str + :param append: Wether to create a neww file or to append to an existing one. + :type append: bool + + """ + mode = 'a' if append else 'w' + titles = [d.title for d in self._datasets] + with h5py.File(filename, mode) as fd: + if append: + try: + data_grp = fd['DATA'] + meta_grp = fd['MsSpec viewer metainfo'] + except Exception as err: + fd.close() + self.save(filename, append=False) + return + else: + data_grp = fd.create_group('DATA') + meta_grp = fd.create_group('MsSpec viewer metainfo') + + data_grp.attrs['title'] = self.title + for dset in self._datasets: + if dset.title in data_grp: + LOGGER.warning('dataset \"{}\" already exists in file \"{}\", not overwritting'.format( + dset.title, os.path.abspath(filename))) + continue + grp = data_grp.create_group(dset.title) + grp.attrs['notes'] = dset.notes + for col_name in dset.columns(): + data = dset[col_name] + grp.create_dataset(col_name, data=data) + + meta_grp.attrs['version'] = msspec.__version__ + + root = etree.Element('metainfo') + # xmlize views + for dset in self._datasets: + views_node = etree.SubElement(root, 'views', dataset=dset.title) + for view in dset.views(): + view_el = etree.fromstring(view.to_xml()) + views_node.append(view_el) + + # xmlize parameters + for dset in self._datasets: + param_node = etree.SubElement(root, 'parameters', dataset=dset.title) + for p in dset.parameters(): + child = etree.SubElement(param_node, 'parameter') + for k, v in list(p.items()): + child.attrib[k] = v + xml_str = etree.tostring(root, pretty_print=False) + try: + del meta_grp['info'] + except: + pass + finally: + meta_grp.create_dataset('info', data=np.array((xml_str,)).view('S1')) + self._dirty = False + LOGGER.info('Data saved in {}'.format(os.path.abspath(filename))) + + def export(self, folder, overwrite=False): + os.makedirs(folder, exist_ok=overwrite) + for dset in self._datasets: + dset_name = dset.title.replace(' ', '_') + p = os.path.join(folder, dset_name) + os.makedirs(p, exist_ok=overwrite) + fname = os.path.join(p, dset_name) + '.txt' + dset.export(fname) + dset.export_views(p) + + @staticmethod + def load(filename): + """Loads an HDF5 file from the disc. + + :param filename: The path to the file to laod. + :type filename: str + :return: A Data object. + :rtype: :py:class:`iodata.Data` + """ + output = Data() + with h5py.File(filename, 'r') as fd: + parameters = {} + views = {} + + output.title = fd['DATA'].attrs['title'] + for dset_name in fd['DATA'] : + parameters[dset_name] = [] + views[dset_name] = [] + dset = output.add_dset(dset_name) + dset.notes = fd['DATA'][dset_name].attrs['notes'] + for h5dset in fd['DATA'][dset_name]: + dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset].value}) + + try: + vfile = LooseVersion(fd['MsSpec viewer metainfo'].attrs['version']) + if vfile > LooseVersion(msspec.__version__): + raise NameError('File was saved with a more recent format') + xml = fd['MsSpec viewer metainfo']['info'].value.tostring() + root = etree.fromstring(xml) + for elt0 in root.iter('parameters'): + dset_name = elt0.attrib['dataset'] + for elt1 in elt0.iter('parameter'): + parameters[dset_name].append(elt1.attrib) + + for elt0 in root.iter('views'): + dset_name = elt0.attrib['dataset'] + for elt1 in elt0.iter('view'): + view = _DataSetView(None, "") + view.from_xml(etree.tostring(elt1)) + views[dset_name].append(view) + + except Exception as err: + print(err) + + + for dset in output: + for v in views[dset.title]: + dset.add_view(v) + for p in parameters[dset.title]: + dset.add_parameter(**p) + + output._dirty = False + return output + + def __iter__(self): + for dset in self._datasets: + yield dset + + def __getitem__(self, key): + try: + titles = [d.title for d in self._datasets] + i = titles.index(key) + except ValueError: + i = key + return self._datasets[i] + + def __len__(self): + return len(self._datasets) + + def __str__(self): + s = str([dset.title for dset in self._datasets]) + return s + + def __repr__(self): + s = "".format(self.title) + return s + + def view(self): + """Pops up a grphical window to show all the defined views of the Data object. + + """ + #app = wx.App(False) + #app.SetAppName('MsSpec Data Viewer') + #frame = _DataWindow(self) + #frame.Show(True) + #app.MainLoop() + #win = _DataWindow(self) + #win.show() + #Gtk.main() + app = _Application(self) + exit_status = app.run(sys.argv) + sys.exit(exit_status) + +class _Application(Gtk.Application): + def __init__(self, data): + Gtk.Application.__init__(self) + self.data = data + + def do_activate(self): + self.win = _DataWindow(self) + self.win.show() + + def do_startup(self): + Gtk.Application.do_startup(self) + self.builder = Gtk.Builder.new_from_string(MENU_XML, -1) + self.set_menubar(self.builder.get_object("menubar")) + + + + + + +class _DataSetView(object): + def __init__(self, dset, name, **plotopts): + assert is_title_valid(name), '\/:*?"<>| are not allowed in the string' + self.title = name + self.dataset = dset + self._plotopts = dict( + title='No title', + xlabel='', ylabel='', grid=True, legend=[], colorbar=False, + projection='rectilinear', xlim=[None, None], ylim=[None, None], + scale='linear', + marker=None, autoscale=False) + self._plotopts.update(plotopts) + self._selection_tags = [] + self._selection_conditions = [] + + def set_plot_options(self, **kwargs): + self._plotopts.update(kwargs) + + def select(self, *args, **kwargs): + condition = kwargs.get('where', 'True') + legend = kwargs.get('legend', '') + index = kwargs.get('index', None) + if index is None: + self._selection_conditions.append(condition) + self._selection_tags.append(args) + self._plotopts['legend'].append(legend) + else: + self._selection_conditions[index] = condition + self._selection_tags[index] = args + self._plotopts['legend'][index] = legend + + def tags(self): + return self._selection_tags + + def get_data(self): + data = [] + for condition, tags in zip(self._selection_conditions, + self._selection_tags): + indices = [] + # replace all occurence of tags + for tag in self.dataset.columns(): + condition = condition.replace(tag, "p['{}']".format(tag)) + + for i, p in enumerate(self.dataset): + if eval(condition): + indices.append(i) + + values = [] + for tag in tags: + values.append(getattr(self.dataset[indices], tag)) + + data.append(values) + return data + + def get_figure(self): + opts = self._plotopts + + figure = Figure() + axes = None + proj = opts['projection'] + scale = opts['scale'] + if proj == 'rectilinear': + axes = figure.add_subplot(111, projection='rectilinear') + elif proj in ('polar', 'ortho', 'stereo'): + axes = figure.add_subplot(111, projection='polar') + + for values, label in zip(self.get_data(), opts['legend']): + # if we have only one column to plot, select a bar graph + if np.shape(values)[0] == 1: + xvalues = list(range(len(values[0]))) + axes.bar(xvalues, values[0], label=label, + picker=5) + axes.set_xticks(xvalues) + else: + if proj in ('ortho', 'stereo'): + theta, phi, Xsec = cols2matrix(*values) + theta_ticks = np.arange(0, 91, 15) + if proj == 'ortho': + R = np.sin(np.radians(theta)) + R_ticks = np.sin(np.radians(theta_ticks)) + elif proj == 'stereo': + R = 2 * np.tan(np.radians(theta/2.)) + R_ticks = 2 * np.tan(np.radians(theta_ticks/2.)) + #R = np.tan(np.radians(theta/2.)) + X, Y = np.meshgrid(np.radians(phi), R) + im = axes.pcolormesh(X, Y, Xsec) + axes.set_yticks(R_ticks) + axes.set_yticklabels(theta_ticks) + + figure.colorbar(im) + + elif proj == 'polar': + values[0] = np.radians(values[0]) + axes.plot(*values, label=label, picker=5, + marker=opts['marker']) + else: + if scale == 'semilogx': + pltcmd = axes.semilogx + elif scale == 'semilogy': + pltcmd = axes.semilogy + elif scale == 'log': + pltcmd = axes.loglog + else: + pltcmd = axes.plot + pltcmd(*values, label=label, picker=5, + marker=opts['marker']) + axes.grid(opts['grid']) + axes.set_title(opts['title']) + axes.set_xlabel(opts['xlabel']) + axes.set_ylabel(opts['ylabel']) + axes.set_xlim(*opts['xlim']) + axes.set_ylim(*opts['ylim']) + if label: + axes.legend() + axes.autoscale(enable=opts['autoscale']) + + canvas = FigureCanvasAgg(figure) + return figure + + def serialize(self): + data = { + 'name': self.title, + 'selection_conditions': self._selection_conditions, + 'selection_tags': self._selection_tags, + 'plotopts': self._plotopts + } + root = etree.Element('root') + + return data + + def to_xml(self): + plotopts = self._plotopts.copy() + legends = plotopts.pop('legend') + + root = etree.Element('view', name=self.title) + for key, value in list(plotopts.items()): + root.attrib[key] = str(value) + #root.attrib['dataset_name'] = self.dataset.title + + for tags, cond, legend in zip(self._selection_tags, + self._selection_conditions, + legends): + curve = etree.SubElement(root, 'curve') + curve.attrib['legend'] = legend + curve.attrib['condition'] = cond + axes = etree.SubElement(curve, 'axes') + for tag in tags: + variable = etree.SubElement(axes, 'axis', name=tag) + + + return etree.tostring(root, pretty_print=False) + + def from_xml(self, xmlstr): + root = etree.fromstring(xmlstr) + self.title = root.attrib['name'] + #self._plotopts['title'] = root.attrib['title'] + #self._plotopts['xlabel'] = root.attrib['xlabel'] + # self._plotopts['ylabel'] = root.attrib['ylabel'] + # self._plotopts['grid'] = bool(root.attrib['grid']) + # self._plotopts['colorbar'] = bool(root.attrib['colorbar']) + # self._plotopts['projection'] = root.attrib['projection'] + # self._plotopts['marker'] = root.attrib['marker'] + for key in list(self._plotopts.keys()): + try: + self._plotopts[key] = eval(root.attrib.get(key)) + except: + self._plotopts[key] = root.attrib.get(key) + + + + legends = [] + conditions = [] + tags = [] + for curve in root.iter("curve"): + legends.append(curve.attrib['legend']) + conditions.append(curve.attrib['condition']) + variables = [] + for var in curve.iter('axis'): + variables.append(var.attrib['name']) + tags.append(tuple(variables)) + + self._selection_conditions = conditions + self._selection_tags = tags + self._plotopts['legend'] = legends + + def __repr__(self): + s = "<{}('{}')>".format(self.__class__.__name__, self.title) + return s + + def __str__(self): + try: + dset_title = self.dataset.title + except AttributeError: + dset_title = "unknown" + s = '{}:\n'.format(self.__class__.__name__) + s += '\tname : %s\n' % self.title + s += '\tdataset : %s\n' % dset_title + s += '\ttags : %s\n' % str(self._selection_tags) + s += '\tconditions : %s\n' % str(self._selection_conditions) + return s + +class _GridWindow(wx.Frame): + def __init__(self, dset, parent=None): + title = 'Data: ' + dset.title + wx.Frame.__init__(self, parent, title=title, size=(640, 480)) + self.create_grid(dset) + + def create_grid(self, dset): + grid = wx.grid.Grid(self, -1) + grid.CreateGrid(len(dset), len(dset.columns())) + for ic, c in enumerate(dset.columns()): + grid.SetColLabelValue(ic, c) + for iv, v in enumerate(dset[c]): + grid.SetCellValue(iv, ic, str(v)) + +class _ParametersWindow(wx.Frame): + def __init__(self, dset, parent=None): + title = 'Parameters: ' + dset.title + wx.Frame.__init__(self, parent, title=title, size=(400, 480)) + self.create_tree(dset) + + def create_tree(self, dset): + datatree = {} + for p in dset.parameters(): + is_hidden = p.get('hidden', "False") + if is_hidden == "True": + continue + group = datatree.get(p['group'], []) + #strval = str(p['value'] * p['unit'] if p['unit'] else p['value']) + #group.append("{:s} = {:s}".format(p['name'], strval)) + group.append("{} = {} {}".format(p['name'], p['value'], p['unit'])) + datatree[p['group']] = group + + tree = wx.TreeCtrl(self, -1) + root = tree.AddRoot('Parameters') + + for key in list(datatree.keys()): + item0 = tree.AppendItem(root, key) + for item in datatree[key]: + tree.AppendItem(item0, item) + tree.ExpandAll() + tree.SelectItem(root) + + + +class _DataWindow(Gtk.ApplicationWindow): + def __init__(self, app): + Gtk.ApplicationWindow.__init__(self, title="MsSpec Data viewer", + application=app) + + data = app.data + assert isinstance(data, (Data, DataSet)) + + if isinstance(data, DataSet): + dset = data + data = Data() + data.first = dset + + self.data = data + self._filename = None + self._current_dset = None + + box = Gtk.Box(orientation=Gtk.Orientation.VERTICAL) + box.show() + self.add(box) + + # connect events + self.connect("delete_event", self.on_close) + + # Create the menu bar + self.create_menu() + + # Create the status bar + sb = self.create_statusbar() + box.pack_end(sb, expand=False, fill=True, padding=2) + + # Create the notebook to hold graphs + self.notebooks = self.create_notebooks() + for nb in self.notebooks.values(): + box.pack_start(nb, expand=True, fill=True, padding=2) + + self.show_dataset(self.data[0].title) + + + + def create_statusbar(self): + sb = Gtk.Statusbar() + ctx = sb.get_context_id("main") + sb.push(ctx, "sb") + sb.show() + return sb + + def create_notebooks(self): + notebooks = {} + for dset in self.data: + nb = Gtk.Notebook() + notebooks[dset.title] = nb + for view in dset.views(): + page = self.create_page(view) + nb.append_page(page, Gtk.Label(label=view.title)) + print("adding ", view.title) + return notebooks + + def create_menu(self): + app = self.get_application() + mb = app.get_menubar() + dset_menu = app.builder.get_object("dset_menu") + + action = Gio.SimpleAction.new("quit", None) + action.connect("activate", self.on_close) + self.add_action(action) + + # create an action + initial_state = GLib.Variant.new_string(data[0].title) + action = Gio.SimpleAction.new_stateful("select_dataset", + initial_state.get_type(), + initial_state) + action.connect("change-state", self.on_menu_dataset) + self.add_action(action) + for dset in self.data: + detailed_action = "win.select_dataset::" + dset.title + item = Gio.MenuItem.new(dset.title, detailed_action) + dset_menu.append_item(item) + + + def create_page(self, view): + # Get the matplotlib figure + figure = view.get_figure() + + # Create a matplotlib canvas for the figure + canvas = FigureCanvas(figure) + canvas.set_size_request(800, 600) + box = Gtk.Box() + box.add(canvas) + + # MPL events + figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion) + figure.canvas.mpl_connect('pick_event', self.on_mpl_pick) + + return box + + + def on_open(self, event): + pass + + def on_save(self, event): + pass + + def on_saveas(self, event): + pass + + def on_export(self, event): + pass + + def on_viewdata(self, event): + pass + + def on_viewcluster(self, event): + pass + + def on_viewparameters(self, event): + pass + + def on_close(self, action, param): + if self.data.is_dirty(): + dlg = Gtk.Dialog(title="Warning: Unsaved data", + transient_for=self, flags=Gtk.DialogFlags.MODAL) + dlg.add_buttons(Gtk.STOCK_YES, Gtk.ResponseType.YES, + Gtk.STOCK_NO, Gtk.ResponseType.NO) + dlg.set_default_size(150, 100) + label = Gtk.Label(label=("Displayed data is unsaved. Do you " + "really want to quit ?")) + icon = Gtk.Image.new_from_icon_name("dialog-warning", + Gtk.IconSize.DIALOG) + area = dlg.get_content_area() + box = Gtk.Box(orientation=Gtk.Orientation.HORIZONTAL) + box.pack_start(icon, expand=False, fill=False, padding=2) + box.pack_start(label, expand=False, fill=False, padding=2) + area.add(box) + dlg.show_all() + + response = dlg.run() + if response == Gtk.ResponseType.YES: + self.get_application().quit() + + dlg.destroy() + return True + + def on_menu_dataset(self, action, value): + action.set_state(value) + self.show_dataset(value.get_string()) + + def on_page_changed(self, event): + pass + + def on_mpl_motion(self, event): + pass + + def on_mpl_pick(self, event): + pass + + def show_dataset(self, name): + for nb in self.notebooks.values(): + nb.hide() + self.notebooks[name].show_all() + + def update_statusbar(self): + pass + + def update_title(self): + pass + + + + + + +class OLD_DataWindow(wx.Frame): + def __init__(self, data): + assert isinstance(data, (Data, DataSet)) + + if isinstance(data, DataSet): + dset = data + data = Data() + data.first = dset + self.data = data + self._filename = None + self._current_dset = None + + wx.Frame.__init__(self, None, title="", size=(640, 480)) + + self.Bind(wx.EVT_CLOSE, self.on_close) + + # Populate the menu bar + self.create_menu() + + # Create the status bar + statusbar = wx.StatusBar(self, -1) + statusbar.SetFieldsCount(3) + statusbar.SetStatusWidths([-2, -1, -1]) + self.SetStatusBar(statusbar) + + # Add the notebook to hold all graphs + self.notebooks = {} + sizer = wx.BoxSizer(wx.VERTICAL) + #sizer.Add(self.notebook) + self.SetSizer(sizer) + + self.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.on_page_changed) + + self.create_notebooks() + + self.update_title() + + def create_notebooks(self): + for key in list(self.notebooks.keys()): + nb = self.notebooks.pop(key) + nb.Destroy() + + for dset in self.data: + nb = wx.Notebook(self, -1) + self.notebooks[dset.title] = nb + #self.GetSizer().Add(nb, 1, wx.ALL|wx.EXPAND) + self.GetSizer().Add(nb, proportion=1, flag=wx.ALL|wx.EXPAND) + for view in dset.views(): + self.create_page(nb, view) + + self.create_menu() + + self.show_dataset(self.data[0].title) + + + def create_menu(self): + menubar = wx.MenuBar() + menu1 = wx.Menu() + menu1.Append(110, "Open\tCtrl+O") + menu1.Append(120, "Save\tCtrl+S") + menu1.Append(130, "Save as...") + menu1.Append(140, "Export\tCtrl+E") + menu1.AppendSeparator() + menu1.Append(199, "Close\tCtrl+Q") + + menu2 = wx.Menu() + for i, dset in enumerate(self.data): + menu_id = 201 + i + menu2.AppendRadioItem(menu_id, dset.title) + self.Bind(wx.EVT_MENU, self.on_menu_dataset, id=menu_id) + + self.Bind(wx.EVT_MENU, self.on_open, id=110) + self.Bind(wx.EVT_MENU, self.on_save, id=120) + self.Bind(wx.EVT_MENU, self.on_saveas, id=130) + self.Bind(wx.EVT_MENU, self.on_export, id=140) + self.Bind(wx.EVT_MENU, self.on_close, id=199) + + + menu3 = wx.Menu() + menu3.Append(301, "Data") + menu3.Append(302, "Cluster") + menu3.Append(303, "Parameters") + + self.Bind(wx.EVT_MENU, self.on_viewdata, id=301) + self.Bind(wx.EVT_MENU, self.on_viewcluster, id=302) + self.Bind(wx.EVT_MENU, self.on_viewparameters, id=303) + + menubar.Append(menu1, "&File") + menubar.Append(menu2, "&Datasets") + menubar.Append(menu3, "&View") + self.SetMenuBar(menubar) + + def on_open(self, event): + if self.data.is_dirty(): + mbx = wx.MessageDialog(self, ('Displayed data is unsaved. Do ' + 'you wish to save before opening' + 'another file ?'), + 'Warning: Unsaved data', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_YES: + self.on_saveas(wx.Event()) + mbx.Destroy() + + wildcard = "HDF5 files (*.hdf5)|*.hdf5" + dlg = wx.FileDialog( + self, message="Open a file...", defaultDir=os.getcwd(), + defaultFile="", wildcard=wildcard, style=wx.FD_OPEN + ) + + if dlg.ShowModal() == wx.ID_OK: + path = dlg.GetPath() + self._filename = path + self.data = Data.load(path) + self.create_notebooks() + dlg.Destroy() + self.update_title() + + def on_save(self, event): + if self._filename: + if self.data.is_dirty(): + self.data.save(self._filename) + else: + self.on_saveas(event) + + def on_saveas(self, event): + overwrite = True + wildcard = "HDF5 files (*.hdf5)|*.hdf5|All files (*.*)|*.*" + dlg = wx.FileDialog( + self, message="Save file as ...", defaultDir=os.getcwd(), + defaultFile='{}.hdf5'.format(self.data.title.replace(' ','_')), + wildcard=wildcard, style=wx.FD_SAVE) + dlg.SetFilterIndex(0) + + if dlg.ShowModal() == wx.ID_OK: + path = dlg.GetPath() + if os.path.exists(path): + mbx = wx.MessageDialog(self, ('This file already exists. ' + 'Do you wish to overwrite it ?'), + 'Warning: File exists', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_NO: + overwrite = False + mbx.Destroy() + if overwrite: + self.data.save(path) + self._filename = path + dlg.Destroy() + self.update_title() + + def on_export(self, event): + overwrite = True + dlg = wx.DirDialog( + self, message="Export data...", defaultPath=os.getcwd(), + style=wx.DD_DEFAULT_STYLE) + + if dlg.ShowModal() == wx.ID_OK: + path = dlg.GetPath() + if os.listdir(path): + mbx = wx.MessageDialog(self, + ('This folder is not empty. ' + 'Exporting tour data here may ' + 'overwrite its content. Do you wish ' + 'to continue ?'), + 'Warning: Folder is not empty', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_NO: + overwrite = False + mbx.Destroy() + self.data.export(path, overwrite) + dlg.Destroy() + + def on_viewdata(self, event): + dset = self.data[self._current_dset] + frame = _GridWindow(dset, parent=self) + frame.Show() + + def on_viewcluster(self, event): + win = wx.Frame(None, size=wx.Size(480, 340)) + cluster_viewer = ClusterViewer(win, size=wx.Size(480, 340)) + + dset = self.data[self._current_dset] + s = StringIO() + s.write(dset.get_parameter(group='Cluster', name='cluster')['value']) + atoms = ase.io.read(s, format='xyz') + cluster_viewer.set_atoms(atoms, rescale=True, center=True) + cluster_viewer.rotate_atoms(0., 180.) + cluster_viewer.rotate_atoms(-45., -45.) + #cluster_viewer.show_emitter(True) + win.Show() + + def on_viewparameters(self, event): + dset = self.data[self._current_dset] + frame = _ParametersWindow(dset, parent=self) + frame.Show() + + def on_close(self, event): + if self.data.is_dirty(): + mbx = wx.MessageDialog(self, ('Displayed data is unsaved. Do you ' + 'really want to quit ?'), + 'Warning: Unsaved data', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_NO: + mbx.Destroy() + return + self.Destroy() + + + def on_menu_dataset(self, event): + menu_id = event.GetId() + dset_name = self.GetMenuBar().FindItemById(menu_id).GetText() + self.show_dataset(dset_name) + + + def show_dataset(self, name): + for nb in list(self.notebooks.values()): + nb.Hide() + self.notebooks[name].Show() + self.Layout() + self.update_statusbar() + self._current_dset = name + + def create_page(self, nb, view): + # Get the matplotlib figure + figure = view.get_figure() + + # Create a panel + p = wx.Panel(nb, -1) + + # Create a matplotlib canvas for the figure + canvas = FigureCanvas(p, -1, figure) + sizer = wx.BoxSizer(wx.VERTICAL) + + toolbar = NavigationToolbar2WxAgg(canvas) + toolbar.Realize() + + #sizer.Add(toolbar, 0, wx.ALL|wx.EXPAND) + sizer.Add(toolbar, proportion=0, flag=wx.ALL|wx.EXPAND) + toolbar.update() + + #sizer.Add(canvas, 5, wx.ALL|wx.EXPAND) + sizer.Add(canvas, proportion=1, flag=wx.ALL|wx.EXPAND) + + p.SetSizer(sizer) + p.Fit() + p.Show() + + # MPL events + figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion) + figure.canvas.mpl_connect('pick_event', self.on_mpl_pick) + + nb.AddPage(p, view.title) + canvas.draw() + + + def OLDcreate_page(self, nb, view): + opts = view._plotopts + p = wx.Panel(nb, -1) + + figure = Figure() + + axes = None + proj = opts['projection'] + scale = opts['scale'] + if proj == 'rectilinear': + axes = figure.add_subplot(111, projection='rectilinear') + elif proj in ('polar', 'ortho', 'stereo'): + axes = figure.add_subplot(111, projection='polar') + + canvas = FigureCanvas(p, -1, figure) + sizer = wx.BoxSizer(wx.VERTICAL) + + toolbar = NavigationToolbar2WxAgg(canvas) + toolbar.Realize() + + sizer.Add(toolbar, 0, wx.ALL|wx.EXPAND) + toolbar.update() + + sizer.Add(canvas, 5, wx.ALL|wx.EXPAND) + + p.SetSizer(sizer) + p.Fit() + p.Show() + + + for values, label in zip(view.get_data(), opts['legend']): + # if we have only one column to plot, select a bar graph + if np.shape(values)[0] == 1: + xvalues = list(range(len(values[0]))) + axes.bar(xvalues, values[0], label=label, + picker=5) + axes.set_xticks(xvalues) + else: + if proj in ('ortho', 'stereo'): + theta, phi, Xsec = cols2matrix(*values) + theta_ticks = np.arange(0, 91, 15) + if proj == 'ortho': + R = np.sin(np.radians(theta)) + R_ticks = np.sin(np.radians(theta_ticks)) + elif proj == 'stereo': + R = 2 * np.tan(np.radians(theta/2.)) + R_ticks = 2 * np.tan(np.radians(theta_ticks/2.)) + #R = np.tan(np.radians(theta/2.)) + X, Y = np.meshgrid(np.radians(phi), R) + im = axes.pcolormesh(X, Y, Xsec) + axes.set_yticks(R_ticks) + axes.set_yticklabels(theta_ticks) + + figure.colorbar(im) + + elif proj == 'polar': + values[0] = np.radians(values[0]) + axes.plot(*values, label=label, picker=5, + marker=opts['marker']) + else: + if scale == 'semilogx': + pltcmd = axes.semilogx + elif scale == 'semilogy': + pltcmd = axes.semilogy + elif scale == 'log': + pltcmd = axes.loglog + else: + pltcmd = axes.plot + pltcmd(*values, label=label, picker=5, + marker=opts['marker']) + axes.grid(opts['grid']) + axes.set_title(opts['title']) + axes.set_xlabel(opts['xlabel']) + axes.set_ylabel(opts['ylabel']) + axes.set_xlim(*opts['xlim']) + axes.set_ylim(*opts['ylim']) + if label: + axes.legend() + axes.autoscale(enable=opts['autoscale']) + + + # MPL events + figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion) + figure.canvas.mpl_connect('pick_event', self.on_mpl_pick) + + nb.AddPage(p, view.title) + + + def update_statusbar(self): + sb = self.GetStatusBar() + menu_id = self.GetMenuBar().FindMenu('Datasets') + menu = self.GetMenuBar().GetMenu(menu_id) + for item in menu.GetMenuItems(): + if item.IsChecked(): + sb.SetStatusText("%s" % item.GetText(), 1) + break + + def update_title(self): + title = "MsSpec Data Viewer" + if self.data.title: + title += ": " + self.data.title + if self._filename: + title += " [" + os.path.basename(self._filename) + "]" + self.SetTitle(title) + + def on_mpl_motion(self, event): + sb = self.GetStatusBar() + try: + txt = "[{:.3f}, {:.3f}]".format(event.xdata, event.ydata) + sb.SetStatusText(txt, 2) + except Exception: + pass + + def on_mpl_pick(self, event): + print(event.artist) + + def on_page_changed(self, event): + self.update_statusbar() + + + + + + + + + + + +if __name__ == "__main__": + if True: + data = Data('all my data') + dset = data.add_dset('Dataset 0') + X = np.arange(0, 20) + Y = X**2 + + dset.add_columns(x=X, y=Y, z=X+2, w=Y**3) + dset.add_parameter(name='truc', group='main', value='3.14', unit='eV') + dset.add_parameter(name='machin', group='main', value='abc', unit='') + + # Z = [0,1] + # + # for z in Z: + # for x, y in zip(X, Y): + # dset.add_row(x=x, y=y, z=z, random=np.random.rand()) + # + # + view = dset.add_view('my view', autoscale=True) + view.select('x', 'y', where="z<10", legend=r"z = 0") + view.select('x', 'y', where="z>10", legend=r"z = 1") + print(dset.get_parameter(group='main')) + constraint = lambda a, b: (a > 10 and a < 15) and b > 0 + indices = list(map(constraint, dset.x, dset.w)) + print(dset.y[indices]) + + view = dset.add_view('my view 2', autoscale=True) + view.select('x', 'y', where="w<30", legend=r"w < 30") + + dset1 = data.add_dset('Dataset 1') + X = np.arange(0, 20) + Y = 2*np.sin(X) + dset1.add_columns(x=X, y=Y) + view = dset1.add_view('my view dset1', autoscale=True) + view.select('x', 'y') + + data.view() + #import sys + #data = Data.load(sys.argv[1]) + #data.view() diff --git a/src/msspec/iodata_wx.py b/src/msspec/iodata_wx.py new file mode 100644 index 0000000..bc1c5b0 --- /dev/null +++ b/src/msspec/iodata_wx.py @@ -0,0 +1,1455 @@ +#!/usr/bin/env python +# +# Copyright © 2016-2020 - Rennes Physics Institute +# +# This file is part of msspec. +# +# msspec is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# msspec is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# You should have received a copy of the GNU General Public License +# along with this msspec. If not, see . +# +# Source file : src/msspec/iodata.py +# Last modified: ven. 10 avril 2020 17:23:11 +# Committed by : "Sylvain Tricot " + + +""" +Module iodata +============= + +This module contains all classes useful to manipulate, store and display +data results. + +The :py:class:`Data` and :py:class:`DataSet` are the two enduser classes +important to manipulate the data. +Here is an example of how to store values in a Data object: + +.. code-block:: python + + from msspec.iodata import Data + import numpy as np + + + # Let's create first some dumy data + X = np.arange(0, 20) + Y = X**2 + + # Create a Data object. You need to give a title as an argument + data = Data('all my data') + # and append a new DataSet with its title + dset = data.add_dset('Dataset 0') + + # To feed the DataSet with columns, use the add_columns method + # and provide as many keywords as you like. Each key being the + # column name and each value being an array holding the column + # data. + dset.add_columns(x=X, y=Y, z=X+2, w=Y**3) + # you can provide parameters with their values with keywords as well + dset.add_parameter(name='truc', group='main', value='3.14', unit='eV') + + # To plot these data, you need to add a 'view' with its title + view = dset.add_view('my view') + # You then need to select which columns you which to plot and + # and under wich conditions (with the 'which' keyword) + view.select('x', 'y', where="z<10", legend=r"z = 0") + view.select('x', 'y', where="z>10", legend=r"z = 1") + + # To pop up the graphical window + data.view() + +""" + + +import os +import sys +from distutils.version import LooseVersion +from distutils.version import StrictVersion +from io import StringIO +from datetime import datetime + +import ase.io +import h5py +import numpy as np +import wx.grid +from lxml import etree +from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas +#from matplotlib.backends.backend_wxagg import FigureCanvasWx as FigureCanvas +from matplotlib.backends.backend_agg import FigureCanvasAgg +from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg +from matplotlib.figure import Figure +from terminaltables import AsciiTable + +import msspec +from msspec.msspecgui.msspec.gui.clusterviewer import ClusterViewer +from msspec.misc import LOGGER + + +def cols2matrix(x, y, z, nx=88*1+1, ny=360*1+1): + # mix the values of existing theta and new theta and return the + # unique values + newx = np.linspace(np.min(x), np.max(x), nx) + newy = np.linspace(np.min(y), np.max(y), ny) + ux = np.unique(np.append(x, newx)) + uy = np.unique(np.append(y, newy)) + + # create an empty matrix to hold the results + zz = np.empty((len(ux), len(uy))) + zz[:] = np.nan + + for p in zip(x, y, z): + i = np.argwhere(ux == p[0]) + j = np.argwhere(uy == p[1]) + zz[i, j] = p[2] + + for i in range(len(ux)): + #ok, = np.where(-np.isnan(zz[i,:])) + ok, = np.where(~np.isnan(zz[i, :])) + if len(ok) > 0: + xp = uy[ok] + fp = zz[i, ok] + zz[i,:] = np.interp(uy, xp, fp) + + for i in range(len(uy)): + #ok, = np.where(-np.isnan(zz[:,i])) + ok, = np.where(~np.isnan(zz[:, i])) + if len(ok) > 0: + xp = ux[ok] + fp = zz[ok, i] + zz[:,i] = np.interp(ux, xp, fp) + + return ux, uy, zz + + +def is_title_valid(title): + """ Ensure the string does not contain special characters: + /\:*?"<>| + """ + special_chars = ('/', '\\', ':', '*', '?', '\"', '<', '>', '|') + for char in special_chars: + if title.find(char) > -1: + return False + return True + + + +class _DataPoint(dict): + def __init__(self, *args, **kwargs): + dict.__init__(self, *args, **kwargs) + + def __getattr__(self, name): + if name in list(self.keys()): + return self[name] + else: + raise AttributeError("'{}' object has no attribute '{}'".format( + self.__class__.__name__, name)) + +class DataSet(object): + """ + This class can create an object to hold column-oriented data. + + :param title: The text used to entitled the dataset + :type title: str + :param notes: Some comments to add to the data + :type notes: str + + """ + def __init__(self, title, notes=""): + assert is_title_valid(title), '\/:*?"<>| are not allowed in the string' + #self._col_names = [] + #self._col_arrays = [] + self.__dict__['_col_names'] = [] + self.__dict__['_col_arrays'] = [] + + self.title = title + self.notes = notes + self._views = [] + self._parameters = [] + self.attributes = {} + + + self._defaults = {'bool': False, 'str': '', 'int': 0, 'float': 0., + 'complex': complex(0)} + self._formats = {bool: '{:s}', str: '{:s}', int: '{:<20d}', + float: '{:<20.10e}', complex: 's'} + self._formats = ((np.integer, '{:<20d}'), + (np.floating, '{:<20.10e}'), + (np.complex, '({0.real:<.10e} {0.imag:<.10e}j)'), + (np.bool, '{:s}'), + (str, '{:s}')) + + + def _empty_array(self, val): + if isinstance(val, str): + t = 'S256' + else: + t = np.dtype(type(val)) + + if isinstance(val, bool): + default = self._defaults['bool'] + elif isinstance(val, str): + default = self._defaults['str'] + elif isinstance(val, int): + default = self._defaults['int'] + elif isinstance(val, float): + default = self._defaults['float'] + elif isinstance(val, complex): + default = self._defaults['complex'] + else: + raise TypeError('Not a supported type') + + return np.array([default]*len(self), dtype=t) + + def add_row(self, **kwargs): + """Add a row of data into the dataset. + + :param kwargs: Each keyword is a column name. The number of keywords (columns) must be coherent with the + number of existing columns. If no column are defined yet, they will be created. + + """ + for k, v in list(kwargs.items()): + if k not in self._col_names: + self._col_names.append(k) + self._col_arrays.append(self._empty_array(v)) + for k, v in list(kwargs.items()): + i = self._col_names.index(k) + arr = self._col_arrays[i] + arr = np.append(arr, v) + self._col_arrays[i] = arr + + def add_columns(self, **kwargs): + """ + Add columns to the dataset. + + You can provide as many columns as you want to this function. This + function can be called several times on the same dataset but each time + with different column names. Column names are given as keywords. + + :Example: + + >>> from iodata import DataSet + >>> dset = DataSet('My Dataset', notes="Just an example") + >>> xdata = range(10) + >>> ydata = [i**2 for i in xdata] + >>> dset.add_columns(x=xdata, y=ydata) + >>> print dset + >>> +-------+ + >>> | x y | + >>> +-------+ + >>> | 0 0 | + >>> | 1 1 | + >>> | 2 4 | + >>> | 3 9 | + >>> | 4 16 | + >>> | 5 25 | + >>> | 6 36 | + >>> | 7 49 | + >>> | 8 64 | + >>> | 9 81 | + >>> +-------+ + + """ + for k, vv in list(kwargs.items()): + assert k not in self._col_names, ("'{}' column already exists" + "".format(k)) + #if len(self) > 0: + # assert len(vv) == len(self), ( + # 'Too many values in the column (max = {})'.format( + # len(self))) + for k, vv in list(kwargs.items()): + arr = np.array(vv) + self._col_names.append(k) + self._col_arrays.append(arr) + + def delete_rows(self, itemspec): + """ + Delete the rows specified with itemspec. + + """ + for i in range(len(self._col_names)): + self._col_arrays[i] = np.delete(self._col_arrays[i], itemspec) + + def delete_columns(self, *tags): + """ + Removes all columns name passed as arguments + + :param tags: column names. + :type tags: str + + """ + for tag in tags: + i = self._col_names.index(tag) + self._col_names.pop(i) + self._col_arrays.pop(i) + + def columns(self): + """ + Get all the column names. + + :return: List of column names. + :rtype: List of str + + """ + return self._col_names + + def add_view(self, name, overwrite=False, **plotopts): + """ + Creates a new view named *name* with specied plot options. + + :param name: name of the view. + :type name: str + :param plotopts: list of keywords for configuring the plots. + :return: a view. + :rtype: :py:class:`iodata._DataSetView` + """ + if overwrite: + self.delete_view(name) + + if isinstance(name, str): + v = _DataSetView(self, name, **plotopts) + else: + v = name + v.dataset = self + self._views.append(v) + return v + + def delete_view(self, name): + view_titles = [_.title for _ in self._views] + try: + i = view_titles.index(name) + self._views.pop(i) + except: + pass + + def views(self): + """Returns all the defined views in the dataset. + + :return: A list of view + :rtype: List of :py:class:`iodata._DataSetView` + """ + return self._views + + def add_parameter(self, **kwargs): + """Add a parameter to store with the dataset. + + :param kwargs: list of keywords with str values. + + These keywords are: + * name: the name of the parameter. + * group: the name of a group it belongs to. + * value: the value of the parameter. + * unit: the unit of the parameter. + + For example: + + .. code-block:: python + + from iodata import DataSet + + mydset = DataSet("Experiment") + mydset.add_parameter(name='Spectrometer', group='misc', value='Omicron', unit='') + + """ + self._parameters.append(kwargs) + + def parameters(self): + """ + Returns the list of defined parameters. + + :return: all parameters defined in the :py:class:`iodata.DataSet` object. + :rtype: List of dict + """ + return self._parameters + + def get_parameter(self, group=None, name=None): + """Retrieves all parameters for a given name and group. + + * If *name* is given and *group* is None, returns all parameters with such a *name* in all groups. + * If *group* is given and *name* is None, returns all parameters in such a *group* + * If both *name* and *group* are None. Returns all parameters (equivalent to + :py:func:`iodata.DataSet.parameters`). + + :param group: The group name or None. + :type group: str + :param name: The parameter's name or None. + :type name: str + :return: A list of parameters. + :rtype: List of dict + """ + p = [] + for _ in self._parameters: + if _['group'] == group or group == None: + if _['name'] == name or name == None: + p.append(_) + return p[0] if len(p) == 1 else p + + def get_cluster(self): + """Get all the atoms in the cluster. + + :return: The cluster + :rtype: :py:class:`ase.Atoms` + """ + s = StringIO() + s.write(self.get_parameter(group='Cluster', name='cluster')['value']) + return ase.io.read(s, format='xyz') + + + def select(self, *args, **kwargs): + condition = kwargs.get('where', 'True') + indices = [] + + def export_views(self, folder): + for view in self.views(): + f = view.get_figure() + fname = os.path.join(folder, view.title) + '.png' + f.savefig(fname) + + + def export(self, filename="", mode="w"): + """Export the DataSet to the given *filename*. + + :param filename: The name of the file. + :type filename: str + + .. warning:: + + Not yet implemented + """ + + rule = '#' * 80 + '\n' + + def header(): + s = '# PARAMETERS:\n' + groups = [] + for p in self.parameters(): + g = p['group'] + if g not in groups: + groups.append(g) + parameters = {} + for group in groups: + parameters[group] = self.get_parameter(group=group) + for k, v in parameters.items(): + if k == 'Cluster': + continue + s += f"# {k}:\n" + if not(isinstance(v, list)): + v = [v,] + for p in v: + s += f"# {p['name']} = {p['value']} {p['unit']}\n" + return s + + colnames = self.columns() + with open(filename, mode) as fd: + # write the date and time of export + now = datetime.now() + fd.write(f"# Data exported on {now}\n") + fd.write(rule) + + # Append notes + fd.write("# NOTES:\n") + for line in self.notes.split('\n'): + fd.write(f"# {line}\n") + fd.write(rule) + + # Append parameters + fd.write(header()) + fd.write(rule) + + # Append the data + fd.write("# DATA:\n") + fd.write("# " + ("{:<20s}" * len(colnames)).format(*colnames + ) + "\n") + for i in range(len(self)): + row = self[i] + for key in row.columns(): + value = row[key][0] + fmt = '{:s}' + #print value + for t, f in self._formats: + if isinstance(value, t): + fmt = f + break + #fd.write(' ') + fd.write(fmt.format(value)) + #fd.write(str(value) + ', ') + fd.write('\n') + + def __getitem__(self, itemspec): + if isinstance(itemspec, str): + return getattr(self, itemspec) + title = 'untitled' + new = DataSet(title) + + new._col_names = self.columns() + for arr in self._col_arrays: + new._col_arrays.append(np.asarray(arr)[itemspec].flatten()) + + return new + + def __setstate__(self, state): + self.__dict__ = state + + def __getstate__(self): + return self.__dict__ + + def __getattr__(self, name): + if name in self._col_names: + i = self._col_names.index(name) + return self._col_arrays[i] + else: + raise AttributeError("'{}' object has no attribute '{}'".format( + self.__class__.__name__, name)) + + def __setattr__(self, name, value): + if name in self._col_names: + i = self._col_names.index(name) + self._col_arrays[i] = value + else: + self.__dict__[name] = value + + def __iter__(self): + for i in range(len(self)): + _ = {k: arr[i] for k, arr in zip(self._col_names, + self._col_arrays)} + point = _DataPoint(_) + yield point + + def __len__(self): + try: + #length = len(self._col_arrays[0]) + length = 0 + for array in self._col_arrays: + length = max(length, len(array)) + except IndexError: + length = 0 + return length + + def __str__(self): + max_len = 10 + max_col = 10 + ncols = min(max_col, len(self._col_arrays)) + table_data = [self._col_names[:ncols]] + table_data[0].insert(0, "") + + all_indices = np.arange(0, len(self)) + indices = all_indices + if len(self) > max_len: + indices = list(range(int(max_len/2))) + list(range(int(-max_len/2), 0)) + + _i = 0 + for i in indices: + if i < _i: + row = ['...' for _ in range(ncols + 1)] + table_data.append(row) + row = [str(all_indices[i]),] + for j in range(ncols): + arr = self._col_arrays[j] + row.append(str(arr[i])) + if len(self._col_names) > max_col: + row.append('...') + table_data.append(row) + _i = i + + table = AsciiTable(table_data) + table.outer_border = True + table.title = self.title + table.inner_column_border = False + return table.table + + def __repr__(self): + s = "<{}('{}')>".format(self.__class__.__name__, self.title) + return s + +class Data(object): + """Creates a new Data object to store DataSets. + + :param title: The title of the Data object. + :type str: + + """ + def __init__(self, title=''): + assert is_title_valid(title), '\/:*?"<>| are not allowed in the string' + self.title = title + self._datasets = [] + self._dirty = False + + def add_dset(self, title, overwrite=False): + """Adds a new DataSet in the Data object. + + :param title: The name of the DataSet. + :type title: str + :param overwrite: Tells whether to re-create the dataset if it exists. + :type overwrite: bool + :return: The newly created DataSet. + :rtype: :py:class:`iodata.DataSet` + """ + if overwrite: + try: + self.delete_dset(title) + except Exception as err: + pass + + titles = [d.title for d in self._datasets] + if not title in titles: + dset = DataSet(title) + self._datasets.append(dset) + self._dirty = True + return dset + else: + raise NameError('A Dataset with that name already exists!') + + def delete_dset(self, title): + """Removes a DataSet from the Data object. + + :param title: The DataSet name to be removed. + :type title: str + + """ + titles = [d.title for d in self._datasets] + i = titles.index(title) + self._datasets.pop(i) + self._dirty = True + + def get_last_dset(self): + """Get the last DataSet of the Data object. + + :return: The lastly created DataSet in the Data object + :rtype: :py:class:`iodata.DataSet` + """ + return self._datasets[-1] + + def is_dirty(self): + """Wether the Data object needs to be saved. + + :return: A boolean value to indicate if Data has changed since last dump to hard drive. + :rtype: bool + """ + return self._dirty + + + def save(self, filename, append=False): + """Saves the current Data to the hard drive. + + The Data, all its content along with parameters, defined views... are saved to the hard drive in the HDF5 + file format. Please see `hdfgroup `_ for more details about HDF5. + + :param filename: The name of the file to create or to append to. + :type filename: str + :param append: Wether to create a neww file or to append to an existing one. + :type append: bool + + """ + mode = 'a' if append else 'w' + titles = [d.title for d in self._datasets] + with h5py.File(filename, mode) as fd: + if append: + try: + data_grp = fd['DATA'] + meta_grp = fd['MsSpec viewer metainfo'] + except Exception as err: + fd.close() + self.save(filename, append=False) + return + else: + data_grp = fd.create_group('DATA') + meta_grp = fd.create_group('MsSpec viewer metainfo') + + data_grp.attrs['title'] = self.title + for dset in self._datasets: + if dset.title in data_grp: + LOGGER.warning('dataset \"{}\" already exists in file \"{}\", not overwritting'.format( + dset.title, os.path.abspath(filename))) + continue + grp = data_grp.create_group(dset.title) + grp.attrs['notes'] = dset.notes + for col_name in dset.columns(): + data = dset[col_name] + grp.create_dataset(col_name, data=data) + + meta_grp.attrs['version'] = msspec.__version__ + + root = etree.Element('metainfo') + # xmlize views + for dset in self._datasets: + views_node = etree.SubElement(root, 'views', dataset=dset.title) + for view in dset.views(): + view_el = etree.fromstring(view.to_xml()) + views_node.append(view_el) + + # xmlize parameters + for dset in self._datasets: + param_node = etree.SubElement(root, 'parameters', dataset=dset.title) + for p in dset.parameters(): + child = etree.SubElement(param_node, 'parameter') + for k, v in list(p.items()): + child.attrib[k] = v + xml_str = etree.tostring(root, pretty_print=False) + try: + del meta_grp['info'] + except: + pass + finally: + meta_grp.create_dataset('info', data=np.array((xml_str,)).view('S1')) + self._dirty = False + LOGGER.info('Data saved in {}'.format(os.path.abspath(filename))) + + def export(self, folder, overwrite=False): + os.makedirs(folder, exist_ok=overwrite) + for dset in self._datasets: + dset_name = dset.title.replace(' ', '_') + p = os.path.join(folder, dset_name) + os.makedirs(p, exist_ok=overwrite) + fname = os.path.join(p, dset_name) + '.txt' + dset.export(fname) + dset.export_views(p) + + @staticmethod + def load(filename): + """Loads an HDF5 file from the disc. + + :param filename: The path to the file to laod. + :type filename: str + :return: A Data object. + :rtype: :py:class:`iodata.Data` + """ + output = Data() + with h5py.File(filename, 'r') as fd: + parameters = {} + views = {} + + output.title = fd['DATA'].attrs['title'] + for dset_name in fd['DATA'] : + parameters[dset_name] = [] + views[dset_name] = [] + dset = output.add_dset(dset_name) + dset.notes = fd['DATA'][dset_name].attrs['notes'] + for h5dset in fd['DATA'][dset_name]: + dset.add_columns(**{h5dset: fd['DATA'][dset_name][h5dset].value}) + + try: + vfile = LooseVersion(fd['MsSpec viewer metainfo'].attrs['version']) + if vfile > LooseVersion(msspec.__version__): + raise NameError('File was saved with a more recent format') + xml = fd['MsSpec viewer metainfo']['info'].value.tostring() + root = etree.fromstring(xml) + for elt0 in root.iter('parameters'): + dset_name = elt0.attrib['dataset'] + for elt1 in elt0.iter('parameter'): + parameters[dset_name].append(elt1.attrib) + + for elt0 in root.iter('views'): + dset_name = elt0.attrib['dataset'] + for elt1 in elt0.iter('view'): + view = _DataSetView(None, "") + view.from_xml(etree.tostring(elt1)) + views[dset_name].append(view) + + except Exception as err: + print(err) + + + for dset in output: + for v in views[dset.title]: + dset.add_view(v) + for p in parameters[dset.title]: + dset.add_parameter(**p) + + output._dirty = False + return output + + def __iter__(self): + for dset in self._datasets: + yield dset + + def __getitem__(self, key): + try: + titles = [d.title for d in self._datasets] + i = titles.index(key) + except ValueError: + i = key + return self._datasets[i] + + def __len__(self): + return len(self._datasets) + + def __str__(self): + s = str([dset.title for dset in self._datasets]) + return s + + def __repr__(self): + s = "".format(self.title) + return s + + def view(self): + """Pops up a grphical window to show all the defined views of the Data object. + + """ + app = wx.App(False) + app.SetAppName('MsSpec Data Viewer') + frame = _DataWindow(self) + frame.Show(True) + app.MainLoop() + + +class _DataSetView(object): + def __init__(self, dset, name, **plotopts): + assert is_title_valid(name), '\/:*?"<>| are not allowed in the string' + self.title = name + self.dataset = dset + self._plotopts = dict( + title='No title', + xlabel='', ylabel='', grid=True, legend=[], colorbar=False, + projection='rectilinear', xlim=[None, None], ylim=[None, None], + scale='linear', + marker=None, autoscale=False) + self._plotopts.update(plotopts) + self._selection_tags = [] + self._selection_conditions = [] + + def set_plot_options(self, **kwargs): + self._plotopts.update(kwargs) + + def select(self, *args, **kwargs): + condition = kwargs.get('where', 'True') + legend = kwargs.get('legend', '') + index = kwargs.get('index', None) + if index is None: + self._selection_conditions.append(condition) + self._selection_tags.append(args) + self._plotopts['legend'].append(legend) + else: + self._selection_conditions[index] = condition + self._selection_tags[index] = args + self._plotopts['legend'][index] = legend + + def tags(self): + return self._selection_tags + + def get_data(self): + data = [] + for condition, tags in zip(self._selection_conditions, + self._selection_tags): + indices = [] + # replace all occurence of tags + for tag in self.dataset.columns(): + condition = condition.replace(tag, "p['{}']".format(tag)) + + for i, p in enumerate(self.dataset): + if eval(condition): + indices.append(i) + + values = [] + for tag in tags: + values.append(getattr(self.dataset[indices], tag)) + + data.append(values) + return data + + def get_figure(self): + opts = self._plotopts + + figure = Figure() + axes = None + proj = opts['projection'] + scale = opts['scale'] + if proj == 'rectilinear': + axes = figure.add_subplot(111, projection='rectilinear') + elif proj in ('polar', 'ortho', 'stereo'): + axes = figure.add_subplot(111, projection='polar') + + for values, label in zip(self.get_data(), opts['legend']): + # if we have only one column to plot, select a bar graph + if np.shape(values)[0] == 1: + xvalues = list(range(len(values[0]))) + axes.bar(xvalues, values[0], label=label, + picker=5) + axes.set_xticks(xvalues) + else: + if proj in ('ortho', 'stereo'): + theta, phi, Xsec = cols2matrix(*values) + theta_ticks = np.arange(0, 91, 15) + if proj == 'ortho': + R = np.sin(np.radians(theta)) + R_ticks = np.sin(np.radians(theta_ticks)) + elif proj == 'stereo': + R = 2 * np.tan(np.radians(theta/2.)) + R_ticks = 2 * np.tan(np.radians(theta_ticks/2.)) + #R = np.tan(np.radians(theta/2.)) + X, Y = np.meshgrid(np.radians(phi), R) + im = axes.pcolormesh(X, Y, Xsec) + axes.set_yticks(R_ticks) + axes.set_yticklabels(theta_ticks) + + figure.colorbar(im) + + elif proj == 'polar': + values[0] = np.radians(values[0]) + axes.plot(*values, label=label, picker=5, + marker=opts['marker']) + else: + if scale == 'semilogx': + pltcmd = axes.semilogx + elif scale == 'semilogy': + pltcmd = axes.semilogy + elif scale == 'log': + pltcmd = axes.loglog + else: + pltcmd = axes.plot + pltcmd(*values, label=label, picker=5, + marker=opts['marker']) + axes.grid(opts['grid']) + axes.set_title(opts['title']) + axes.set_xlabel(opts['xlabel']) + axes.set_ylabel(opts['ylabel']) + axes.set_xlim(*opts['xlim']) + axes.set_ylim(*opts['ylim']) + if label: + axes.legend() + axes.autoscale(enable=opts['autoscale']) + + canvas = FigureCanvasAgg(figure) + return figure + + def serialize(self): + data = { + 'name': self.title, + 'selection_conditions': self._selection_conditions, + 'selection_tags': self._selection_tags, + 'plotopts': self._plotopts + } + root = etree.Element('root') + + return data + + def to_xml(self): + plotopts = self._plotopts.copy() + legends = plotopts.pop('legend') + + root = etree.Element('view', name=self.title) + for key, value in list(plotopts.items()): + root.attrib[key] = str(value) + #root.attrib['dataset_name'] = self.dataset.title + + for tags, cond, legend in zip(self._selection_tags, + self._selection_conditions, + legends): + curve = etree.SubElement(root, 'curve') + curve.attrib['legend'] = legend + curve.attrib['condition'] = cond + axes = etree.SubElement(curve, 'axes') + for tag in tags: + variable = etree.SubElement(axes, 'axis', name=tag) + + + return etree.tostring(root, pretty_print=False) + + def from_xml(self, xmlstr): + root = etree.fromstring(xmlstr) + self.title = root.attrib['name'] + #self._plotopts['title'] = root.attrib['title'] + #self._plotopts['xlabel'] = root.attrib['xlabel'] + # self._plotopts['ylabel'] = root.attrib['ylabel'] + # self._plotopts['grid'] = bool(root.attrib['grid']) + # self._plotopts['colorbar'] = bool(root.attrib['colorbar']) + # self._plotopts['projection'] = root.attrib['projection'] + # self._plotopts['marker'] = root.attrib['marker'] + for key in list(self._plotopts.keys()): + try: + self._plotopts[key] = eval(root.attrib.get(key)) + except: + self._plotopts[key] = root.attrib.get(key) + + + + legends = [] + conditions = [] + tags = [] + for curve in root.iter("curve"): + legends.append(curve.attrib['legend']) + conditions.append(curve.attrib['condition']) + variables = [] + for var in curve.iter('axis'): + variables.append(var.attrib['name']) + tags.append(tuple(variables)) + + self._selection_conditions = conditions + self._selection_tags = tags + self._plotopts['legend'] = legends + + def __repr__(self): + s = "<{}('{}')>".format(self.__class__.__name__, self.title) + return s + + def __str__(self): + try: + dset_title = self.dataset.title + except AttributeError: + dset_title = "unknown" + s = '{}:\n'.format(self.__class__.__name__) + s += '\tname : %s\n' % self.title + s += '\tdataset : %s\n' % dset_title + s += '\ttags : %s\n' % str(self._selection_tags) + s += '\tconditions : %s\n' % str(self._selection_conditions) + return s + +class _GridWindow(wx.Frame): + def __init__(self, dset, parent=None): + title = 'Data: ' + dset.title + wx.Frame.__init__(self, parent, title=title, size=(640, 480)) + self.create_grid(dset) + + def create_grid(self, dset): + grid = wx.grid.Grid(self, -1) + grid.CreateGrid(len(dset), len(dset.columns())) + for ic, c in enumerate(dset.columns()): + grid.SetColLabelValue(ic, c) + for iv, v in enumerate(dset[c]): + grid.SetCellValue(iv, ic, str(v)) + +class _ParametersWindow(wx.Frame): + def __init__(self, dset, parent=None): + title = 'Parameters: ' + dset.title + wx.Frame.__init__(self, parent, title=title, size=(400, 480)) + self.create_tree(dset) + + def create_tree(self, dset): + datatree = {} + for p in dset.parameters(): + is_hidden = p.get('hidden', "False") + if is_hidden == "True": + continue + group = datatree.get(p['group'], []) + #strval = str(p['value'] * p['unit'] if p['unit'] else p['value']) + #group.append("{:s} = {:s}".format(p['name'], strval)) + group.append("{} = {} {}".format(p['name'], p['value'], p['unit'])) + datatree[p['group']] = group + + tree = wx.TreeCtrl(self, -1) + root = tree.AddRoot('Parameters') + + for key in list(datatree.keys()): + item0 = tree.AppendItem(root, key) + for item in datatree[key]: + tree.AppendItem(item0, item) + tree.ExpandAll() + tree.SelectItem(root) + +class _DataWindow(wx.Frame): + def __init__(self, data): + assert isinstance(data, (Data, DataSet)) + + if isinstance(data, DataSet): + dset = data + data = Data() + data.first = dset + self.data = data + self._filename = None + self._current_dset = None + + wx.Frame.__init__(self, None, title="", size=(640, 480)) + + self.Bind(wx.EVT_CLOSE, self.on_close) + + # Populate the menu bar + self.create_menu() + + # Create the status bar + statusbar = wx.StatusBar(self, -1) + statusbar.SetFieldsCount(3) + statusbar.SetStatusWidths([-2, -1, -1]) + self.SetStatusBar(statusbar) + + # Add the notebook to hold all graphs + self.notebooks = {} + sizer = wx.BoxSizer(wx.VERTICAL) + #sizer.Add(self.notebook) + self.SetSizer(sizer) + + self.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.on_page_changed) + + self.create_notebooks() + + self.update_title() + + def create_notebooks(self): + for key in list(self.notebooks.keys()): + nb = self.notebooks.pop(key) + nb.Destroy() + + for dset in self.data: + nb = wx.Notebook(self, -1) + self.notebooks[dset.title] = nb + #self.GetSizer().Add(nb, 1, wx.ALL|wx.EXPAND) + self.GetSizer().Add(nb, proportion=1, flag=wx.ALL|wx.EXPAND) + for view in dset.views(): + self.create_page(nb, view) + + self.create_menu() + + self.show_dataset(self.data[0].title) + + + def create_menu(self): + menubar = wx.MenuBar() + menu1 = wx.Menu() + menu1.Append(110, "Open\tCtrl+O") + menu1.Append(120, "Save\tCtrl+S") + menu1.Append(130, "Save as...") + menu1.Append(140, "Export\tCtrl+E") + menu1.AppendSeparator() + menu1.Append(199, "Close\tCtrl+Q") + + menu2 = wx.Menu() + for i, dset in enumerate(self.data): + menu_id = 201 + i + menu2.AppendRadioItem(menu_id, dset.title) + self.Bind(wx.EVT_MENU, self.on_menu_dataset, id=menu_id) + + self.Bind(wx.EVT_MENU, self.on_open, id=110) + self.Bind(wx.EVT_MENU, self.on_save, id=120) + self.Bind(wx.EVT_MENU, self.on_saveas, id=130) + self.Bind(wx.EVT_MENU, self.on_export, id=140) + self.Bind(wx.EVT_MENU, self.on_close, id=199) + + + menu3 = wx.Menu() + menu3.Append(301, "Data") + menu3.Append(302, "Cluster") + menu3.Append(303, "Parameters") + + self.Bind(wx.EVT_MENU, self.on_viewdata, id=301) + self.Bind(wx.EVT_MENU, self.on_viewcluster, id=302) + self.Bind(wx.EVT_MENU, self.on_viewparameters, id=303) + + menubar.Append(menu1, "&File") + menubar.Append(menu2, "&Datasets") + menubar.Append(menu3, "&View") + self.SetMenuBar(menubar) + + def on_open(self, event): + if self.data.is_dirty(): + mbx = wx.MessageDialog(self, ('Displayed data is unsaved. Do ' + 'you wish to save before opening' + 'another file ?'), + 'Warning: Unsaved data', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_YES: + self.on_saveas(wx.Event()) + mbx.Destroy() + + wildcard = "HDF5 files (*.hdf5)|*.hdf5" + dlg = wx.FileDialog( + self, message="Open a file...", defaultDir=os.getcwd(), + defaultFile="", wildcard=wildcard, style=wx.FD_OPEN + ) + + if dlg.ShowModal() == wx.ID_OK: + path = dlg.GetPath() + self._filename = path + self.data = Data.load(path) + self.create_notebooks() + dlg.Destroy() + self.update_title() + + def on_save(self, event): + if self._filename: + if self.data.is_dirty(): + self.data.save(self._filename) + else: + self.on_saveas(event) + + def on_saveas(self, event): + overwrite = True + wildcard = "HDF5 files (*.hdf5)|*.hdf5|All files (*.*)|*.*" + dlg = wx.FileDialog( + self, message="Save file as ...", defaultDir=os.getcwd(), + defaultFile='{}.hdf5'.format(self.data.title.replace(' ','_')), + wildcard=wildcard, style=wx.FD_SAVE) + dlg.SetFilterIndex(0) + + if dlg.ShowModal() == wx.ID_OK: + path = dlg.GetPath() + if os.path.exists(path): + mbx = wx.MessageDialog(self, ('This file already exists. ' + 'Do you wish to overwrite it ?'), + 'Warning: File exists', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_NO: + overwrite = False + mbx.Destroy() + if overwrite: + self.data.save(path) + self._filename = path + dlg.Destroy() + self.update_title() + + def on_export(self, event): + overwrite = True + dlg = wx.DirDialog( + self, message="Export data...", defaultPath=os.getcwd(), + style=wx.DD_DEFAULT_STYLE) + + if dlg.ShowModal() == wx.ID_OK: + path = dlg.GetPath() + if os.listdir(path): + mbx = wx.MessageDialog(self, + ('This folder is not empty. ' + 'Exporting tour data here may ' + 'overwrite its content. Do you wish ' + 'to continue ?'), + 'Warning: Folder is not empty', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_NO: + overwrite = False + mbx.Destroy() + self.data.export(path, overwrite) + dlg.Destroy() + + def on_viewdata(self, event): + dset = self.data[self._current_dset] + frame = _GridWindow(dset, parent=self) + frame.Show() + + def on_viewcluster(self, event): + win = wx.Frame(None, size=wx.Size(480, 340)) + cluster_viewer = ClusterViewer(win, size=wx.Size(480, 340)) + + dset = self.data[self._current_dset] + s = StringIO() + s.write(dset.get_parameter(group='Cluster', name='cluster')['value']) + atoms = ase.io.read(s, format='xyz') + cluster_viewer.set_atoms(atoms, rescale=True, center=True) + cluster_viewer.rotate_atoms(0., 180.) + cluster_viewer.rotate_atoms(-45., -45.) + #cluster_viewer.show_emitter(True) + win.Show() + + def on_viewparameters(self, event): + dset = self.data[self._current_dset] + frame = _ParametersWindow(dset, parent=self) + frame.Show() + + def on_close(self, event): + if self.data.is_dirty(): + mbx = wx.MessageDialog(self, ('Displayed data is unsaved. Do you ' + 'really want to quit ?'), + 'Warning: Unsaved data', + wx.YES_NO | wx.ICON_WARNING) + if mbx.ShowModal() == wx.ID_NO: + mbx.Destroy() + return + self.Destroy() + + + def on_menu_dataset(self, event): + menu_id = event.GetId() + dset_name = self.GetMenuBar().FindItemById(menu_id).GetText() + self.show_dataset(dset_name) + + + def show_dataset(self, name): + for nb in list(self.notebooks.values()): + nb.Hide() + self.notebooks[name].Show() + self.Layout() + self.update_statusbar() + self._current_dset = name + + def create_page(self, nb, view): + # Get the matplotlib figure + figure = view.get_figure() + + # Create a panel + p = wx.Panel(nb, -1) + + # Create a matplotlib canvas for the figure + canvas = FigureCanvas(p, -1, figure) + sizer = wx.BoxSizer(wx.VERTICAL) + + toolbar = NavigationToolbar2WxAgg(canvas) + toolbar.Realize() + + #sizer.Add(toolbar, 0, wx.ALL|wx.EXPAND) + sizer.Add(toolbar, proportion=0, flag=wx.ALL|wx.EXPAND) + toolbar.update() + + #sizer.Add(canvas, 5, wx.ALL|wx.EXPAND) + sizer.Add(canvas, proportion=1, flag=wx.ALL|wx.EXPAND) + + p.SetSizer(sizer) + p.Fit() + p.Show() + + # MPL events + figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion) + figure.canvas.mpl_connect('pick_event', self.on_mpl_pick) + + nb.AddPage(p, view.title) + canvas.draw() + + + def OLDcreate_page(self, nb, view): + opts = view._plotopts + p = wx.Panel(nb, -1) + + figure = Figure() + + axes = None + proj = opts['projection'] + scale = opts['scale'] + if proj == 'rectilinear': + axes = figure.add_subplot(111, projection='rectilinear') + elif proj in ('polar', 'ortho', 'stereo'): + axes = figure.add_subplot(111, projection='polar') + + canvas = FigureCanvas(p, -1, figure) + sizer = wx.BoxSizer(wx.VERTICAL) + + toolbar = NavigationToolbar2WxAgg(canvas) + toolbar.Realize() + + sizer.Add(toolbar, 0, wx.ALL|wx.EXPAND) + toolbar.update() + + sizer.Add(canvas, 5, wx.ALL|wx.EXPAND) + + p.SetSizer(sizer) + p.Fit() + p.Show() + + + for values, label in zip(view.get_data(), opts['legend']): + # if we have only one column to plot, select a bar graph + if np.shape(values)[0] == 1: + xvalues = list(range(len(values[0]))) + axes.bar(xvalues, values[0], label=label, + picker=5) + axes.set_xticks(xvalues) + else: + if proj in ('ortho', 'stereo'): + theta, phi, Xsec = cols2matrix(*values) + theta_ticks = np.arange(0, 91, 15) + if proj == 'ortho': + R = np.sin(np.radians(theta)) + R_ticks = np.sin(np.radians(theta_ticks)) + elif proj == 'stereo': + R = 2 * np.tan(np.radians(theta/2.)) + R_ticks = 2 * np.tan(np.radians(theta_ticks/2.)) + #R = np.tan(np.radians(theta/2.)) + X, Y = np.meshgrid(np.radians(phi), R) + im = axes.pcolormesh(X, Y, Xsec) + axes.set_yticks(R_ticks) + axes.set_yticklabels(theta_ticks) + + figure.colorbar(im) + + elif proj == 'polar': + values[0] = np.radians(values[0]) + axes.plot(*values, label=label, picker=5, + marker=opts['marker']) + else: + if scale == 'semilogx': + pltcmd = axes.semilogx + elif scale == 'semilogy': + pltcmd = axes.semilogy + elif scale == 'log': + pltcmd = axes.loglog + else: + pltcmd = axes.plot + pltcmd(*values, label=label, picker=5, + marker=opts['marker']) + axes.grid(opts['grid']) + axes.set_title(opts['title']) + axes.set_xlabel(opts['xlabel']) + axes.set_ylabel(opts['ylabel']) + axes.set_xlim(*opts['xlim']) + axes.set_ylim(*opts['ylim']) + if label: + axes.legend() + axes.autoscale(enable=opts['autoscale']) + + + # MPL events + figure.canvas.mpl_connect('motion_notify_event', self.on_mpl_motion) + figure.canvas.mpl_connect('pick_event', self.on_mpl_pick) + + nb.AddPage(p, view.title) + + + def update_statusbar(self): + sb = self.GetStatusBar() + menu_id = self.GetMenuBar().FindMenu('Datasets') + menu = self.GetMenuBar().GetMenu(menu_id) + for item in menu.GetMenuItems(): + if item.IsChecked(): + sb.SetStatusText("%s" % item.GetText(), 1) + break + + def update_title(self): + title = "MsSpec Data Viewer" + if self.data.title: + title += ": " + self.data.title + if self._filename: + title += " [" + os.path.basename(self._filename) + "]" + self.SetTitle(title) + + def on_mpl_motion(self, event): + sb = self.GetStatusBar() + try: + txt = "[{:.3f}, {:.3f}]".format(event.xdata, event.ydata) + sb.SetStatusText(txt, 2) + except Exception: + pass + + def on_mpl_pick(self, event): + print(event.artist) + + def on_page_changed(self, event): + self.update_statusbar() + + + + + + + + + + + +if __name__ == "__main__": + if True: + data = Data('all my data') + dset = data.add_dset('Dataset 0') + X = np.arange(0, 20) + Y = X**2 + + dset.add_columns(x=X, y=Y, z=X+2, w=Y**3) + dset.add_parameter(name='truc', group='main', value='3.14', unit='eV') + dset.add_parameter(name='machin', group='main', value='abc', unit='') + + # Z = [0,1] + # + # for z in Z: + # for x, y in zip(X, Y): + # dset.add_row(x=x, y=y, z=z, random=np.random.rand()) + # + # + view = dset.add_view('my view', autoscale=True) + view.select('x', 'y', where="z<10", legend=r"z = 0") + view.select('x', 'y', where="z>10", legend=r"z = 1") + print(dset.get_parameter(group='main')) + constraint = lambda a, b: (a > 10 and a < 15) and b > 0 + indices = list(map(constraint, dset.x, dset.w)) + print(dset.y[indices]) + + data.view() + #import sys + #data = Data.load(sys.argv[1]) + #data.view()