pyTEMlib 0.2023.3.0__py2.py3-none-any.whl → 0.2023.8.0__py2.py3-none-any.whl

pyTEMlib/peak_dlg.py

@@ -14,14 +14,14 @@ try:
 
 except:
     Qt_available = False
-    print('Qt dialogs are not available')
+    # print('Qt dialogs are not available')
 
 
 if Qt_available:
     class UiDialog(object):
         """GUI definitions for peak_fit_dialog"""
 
-        def __init__(self, dialog):
+        def __init__(self, dialog, mode=None):
             dialog.setObjectName('Fit Peaks')
             dialog.resize(371, 184)
 
@@ -224,30 +224,59 @@ if Qt_available:
             self.separator3.setText("Analysis")
             self.layout.addWidget(self.separator3, row, 0, 1, 4)
             ######################################################################
+            if mode == 'low_loss':
+                row += 1
+                self.zl_button = QtWidgets.QPushButton('Zero_Loss', dialog)
+                self.zl_button.setCheckable(False)
+                self.drude_button = QtWidgets.QPushButton('Plasmon', dialog)
+                self.drude_button.setCheckable(False)
+
+
+                self.layout.addWidget(self.zl_button, row, 0)
+                self.layout.addWidget(self.drude_button, row, 1)
+
+                self.model_list = ['None', 'Zero Loss', 'Plasmon', 'Both']
+                self.list_model = QtWidgets.QComboBox()
+                self.list_model.setEditable(False)
+                self.list_model.addItems(self.model_list)
+                
+
+                self.layout.addWidget(self.list_model, row, 2)
+                
+            else:
+                row += 1
+                self.labelwl = QtWidgets.QLabel('White-Line Ratio:')
+                self.wl_list = ['Ratio']
+                self.listwl = QtWidgets.QComboBox()
+                self.listwl.setEditable(False)
+                self.listwl.addItems(self.wl_list)
+                self.unitswl = QtWidgets.QLabel('')
+
+                self.layout.addWidget(self.labelwl, row, 0)
+                self.layout.addWidget(self.listwl, row, 1)
+                self.layout.addWidget(self.unitswl, row, 2)
+
+                row += 1
+                self.labelwls = QtWidgets.QLabel('White-Line Sum:')
+                self.wls_list = ['Sum']
+                self.listwls = QtWidgets.QComboBox()
+                self.listwls.setEditable(False)
+                self.listwls.addItems(self.wls_list)
+                self.unitswls = QtWidgets.QLabel('')
+
+                self.layout.addWidget(self.labelwls, row, 0)
+                self.layout.addWidget(self.listwls, row, 1)
+                self.layout.addWidget(self.unitswls, row, 2)
 
             row += 1
-            self.labelwl = QtWidgets.QLabel('White-Line Ratio:')
-            self.wl_list = ['Ratio']
-            self.listwl = QtWidgets.QComboBox()
-            self.listwl.setEditable(False)
-            self.listwl.addItems(self.wl_list)
-            self.unitswl = QtWidgets.QLabel('')
-
-            self.layout.addWidget(self.labelwl, row, 0)
-            self.layout.addWidget(self.listwl, row, 1)
-            self.layout.addWidget(self.unitswl, row, 2)
-
-            row += 1
-            self.labelwls = QtWidgets.QLabel('White-Line Sum:')
-            self.wls_list = ['Sum']
-            self.listwls = QtWidgets.QComboBox()
-            self.listwls.setEditable(False)
-            self.listwls.addItems(self.wls_list)
-            self.unitswls = QtWidgets.QLabel('')
-
-            self.layout.addWidget(self.labelwls, row, 0)
-            self.layout.addWidget(self.listwls, row, 1)
-            self.layout.addWidget(self.unitswls, row, 2)
+            self.progress = QtWidgets.QProgressBar()
+            self.progress.setGeometry(0, 0, 300, 25)
+            self.progress.setMaximum(100)
+            self.do_all_button = QtWidgets.QPushButton('Do All', dialog)
+
+            self.layout.addWidget(self.do_all_button, row, 0)
+            self.layout.addWidget(self.progress, row, 1)
+    
 
             dialog.setLayout(self.layout)
             dialog.setWindowTitle('Peak Fit Input')

pyTEMlib/version.py

@@ -1,6 +1,6 @@
 """
 version
 """
-_version = '0.2023.3.0'
+_version = '0.2023.8.0'
 __version__ = _version
-_time = '2023-02-04 19:58:26'
+_time = '2023-08-09 19:58:26'

pyTEMlib/viz.py

@@ -2,6 +2,16 @@
 
 import numpy as np
 import sidpy
+from sidpy.hdf.dtype_utils import is_complex_dtype
+
+import plotly.graph_objects as go
+from plotly.subplots import make_subplots
+from ipywidgets import widgets
+
+
+import pyTEMlib.eels_tools as eels
+import pyTEMlib.file_tools as ft
+
 
 from bokeh.layouts import column
 from bokeh.plotting import figure  # , show, output_notebook
@@ -262,3 +272,210 @@ class CurveVisualizer(object):
         else:
             legline.set_alpha(0.2)
         self.fig.canvas.draw()
+
+        
+def verify_spectrum_dataset(datasets):
+    if isinstance(datasets, sidpy.Dataset):
+        datasets = {'Channel_000': datasets}
+    
+    first_dataset = datasets[list(datasets)[0]]
+    has_complex_dataset = False
+    for dat in datasets.values():
+         if is_complex_dtype(dat.dtype):
+             has_complex_dataset = True
+    
+             
+    if first_dataset.data_type.name != 'SPECTRUM':
+        raise TypeError('We need a spectrum dataset here')
+    if first_dataset.ndim >1:
+        if first_dataset.shape[1] >1:
+            raise TypeError('Wrong dimensions for spectrum datasset')
+    
+    energy_dim = first_dataset.get_spectrum_dims()
+    energy_dim = first_dataset.get_dimension_by_number(energy_dim[0])[0]
+    energy_dim.label = f'{energy_dim.quantity} ({energy_dim.units})'
+    
+    default_plot_dictionary = {'title': '',
+                                'theme': "plotly_white",
+                                'y_scale': 1.0,
+                                'y_axis_label': first_dataset.data_descriptor,
+                                'x_axis_label': energy_dim.label,
+                                'show_legend': True,
+                                'height': 500,
+                                'figure_size': None,
+                                'scale_bar': False,
+                                'colorbar': True,
+                                'set_title': True,
+                                'has_complex_dataset': has_complex_dataset}
+        
+    
+    default_plot_dictionary.update(first_dataset.metadata['plot_parameter'])
+    first_dataset.metadata['plot_parameter'] = default_plot_dictionary
+            
+    return datasets
+
+def spectrum_view_plotly(datasets, figure=None, show=False):
+   
+    datasets =  verify_spectrum_dataset(datasets)
+    first_dataset = datasets[list(datasets)[0]]
+    plot_dic = first_dataset.metadata['plot_parameter']
+    
+    if figure is None:
+        if plot_dic['has_complex_dataset']:
+            fig = make_subplots(rows=1, cols=2, subplot_titles=("Magnitude", "Phase"))
+        else:
+            fig = go.Figure()
+
+    else:
+        fig = figure
+
+    for key, dat in datasets.items():
+        if dat.data_type == first_dataset.data_type:
+            energy_dim = dat.get_spectrum_dims()
+            energy_dim = dat.get_dimension_by_number(energy_dim[0])[0]
+            if is_complex_dtype(dat.dtype):
+               fig.add_trace(go.Scatter(x=energy_dim.values, y=np.abs(dat).squeeze()*plot_dic['y_scale'], name=f'{dat.title}-Magnitude', mode="lines+markers", marker=dict(size=2)), row=1, col=1)
+               fig.add_trace(go.Scatter(x=energy_dim.values, y=np.angle(dat).squeeze()*plot_dic['y_scale'], name=f'{dat.title}-Phase', mode="lines+markers", marker=dict(size=2)), row=1, col=2)
+            else:
+                fig.add_trace(go.Scatter(x=energy_dim.values, y=np.array(dat).squeeze()*plot_dic['y_scale'], name=dat.title, mode="lines+markers", marker=dict(size=2)))
+           
+
+    fig.update_layout(
+        selectdirection='h',
+        showlegend = plot_dic['show_legend'],
+        dragmode='select',
+        title_text=plot_dic['title'],
+        yaxis_title_text=plot_dic['y_axis_label'],
+        xaxis_title_text=plot_dic['x_axis_label'],
+        height=plot_dic['height'],
+        template=plot_dic['theme']
+    )
+    fig.update_layout(hovermode='x unified')
+    
+    if plot_dic['has_complex_dataset']:
+        fig.update_yaxes(title_text='angle (rad)', row = 1, col = 2)
+        fig.update_xaxes(title_text=plot_dic['x_axis_label'], row = 1, col = 2)
+
+    config = {'displayModeBar': True}
+    if show:
+        fig.show(config=config)
+    return fig
+
+
+class SpectrumView(object):
+    def __init__(self, datasets, figure=None, **kwargs):
+        first_dataset = datasets[list(datasets)[0]]
+        if first_dataset.data_type.name != 'SPECTRUM':
+            raise TypeError('We need a spectrum dataset here')
+        if first_dataset.ndim >1:
+            if first_dataset.shape[1] >1:
+                raise TypeError('Wrong dimensions for spectrum datasset')
+        
+        energy_dim = first_dataset.get_spectrum_dims()
+        energy_dim = first_dataset.get_dimension_by_number(energy_dim[0])[0]
+
+        if 'plot_parameter' not in first_dataset.metadata:
+            first_dataset.metadata['plot_parameter'] = {}
+        plot_dic = first_dataset.metadata['plot_parameter']
+        energy_dim.label = f'{energy_dim.quantity} ({energy_dim.units})'
+
+        plot_dic['title'] = kwargs.pop('title', '')
+        plot_dic['theme'] = kwargs.pop('theme', "plotly_white")
+        plot_dic['y_scale'] = kwargs.pop('y_scale', 1.0)
+        plot_dic['y_axis_label'] = kwargs.pop('y_axis_label', first_dataset.data_descriptor)
+        plot_dic['x_axis_label'] = kwargs.pop('x_axis_label', energy_dim.label)
+        plot_dic['height'] = kwargs.pop('height', 500)
+    
+
+        if 'incident_beam_current_counts' in first_dataset.metadata['experiment']:
+            plot_dic['y_scale'] = 1e6/first_dataset.metadata['experiment']['incident_beam_current_counts']
+            plot_dic['y_axis_label'] = ' probability (ppm)'
+        # plot_dic['y_scale'] = 1e6/first_dataset.sum()
+
+        def selection_fn(trace,points,selector):
+            self.energy_selection = [points.point_inds[0], points.point_inds[-1]]
+
+        self.fig = spectrum_view_plotly(datasets)
+
+        self.spectrum_widget = go.FigureWidget(self.fig)
+
+        self.spectrum_widget.data[0].on_selection(selection_fn)
+        self.spectrum_widget.data[0].on_click(self.identify_edges)
+
+        self.edge_annotation = 0
+        self.edge_line = 0
+        self.regions = {}
+        self.initialize_edge()
+
+        self.plot = display(self.spectrum_widget)
+
+    def initialize_edge(self):
+        """ Intitalizes edge cursor
+            Should be run first so that edge cursor is first
+        """
+        self.edge_annotation = len(self.spectrum_widget.layout.annotations)
+        self.edge_line = len(self.spectrum_widget.layout.shapes)
+        self.spectrum_widget.add_vline(x=200, line_dash="dot", line_color='blue',
+                    annotation_text= " ", 
+                    annotation_position="top right",
+                    visible = False)
+
+    def identify_edges(self, trace, points, selector):
+        energy = points.xs[0]
+        edge_names = find_edge_names(points.xs[0])
+        self.spectrum_widget.layout['annotations'][self.edge_annotation].x=energy
+        
+        self.spectrum_widget.layout['annotations'][self.edge_annotation].text = f"{edge_names}"
+        self.spectrum_widget.layout['annotations'][self.edge_annotation].visible = True
+        self.spectrum_widget.layout['shapes'][self.edge_line].x0 = energy
+        self.spectrum_widget.layout['shapes'][self.edge_line].x1 = energy
+        self.spectrum_widget.layout['shapes'][self.edge_line].visible = True
+        self.spectrum_widget.layout.update()
+
+    def add_region(self,  text, start, end, color='blue'): 
+        if text not in self.regions:
+            self.regions[text] = {'annotation': len(self.spectrum_widget.layout.annotations),
+                                'shape': len(self.spectrum_widget.layout.shapes),
+                                'start': start,
+                                'end': end,
+                                'color': color}
+            self.spectrum_widget.add_vrect(x0=start, x1=end, 
+                annotation_text=text, annotation_position="top left",
+                fillcolor=color, opacity=0.15, line_width=0)
+            self.spectrum_widget.layout.update()
+        else:
+            self.update_region(text, start, end)
+
+
+    def update_region(self, text, start, end): 
+        if text in self.regions:
+            region =  self.regions[text]
+            self.spectrum_widget.layout.annotations[region['annotation']].x =start
+            self.spectrum_widget.layout['shapes'][region['shape']].x0 = start
+            self.spectrum_widget.layout['shapes'][region['shape']].x1 = end
+            self.spectrum_widget.layout.update()
+
+    def regions_visibility(self, visibility=True):
+
+        for region in self.regions.values():
+            self.spectrum_widget.layout.annotations[region['annotation']].visible = visibility
+            self.spectrum_widget.layout.shapes[region['shape']].visible = visibility
+
+
+def find_edge_names(energy_value):
+
+    selected_edges = []
+    for shift in [1,2,5,10,20]:
+        selected_edge = ''
+        edges = eels.find_major_edges(energy_value, shift)
+        edges = edges.split('\n')
+        for edge in edges[1:]:
+            edge = edge[:-3].split(':')
+            name = edge[0].strip()
+            energy = float(edge[1].strip())
+            selected_edge = name
+
+            if selected_edge != '':
+                selected_edges.append(selected_edge)
+        if len(selected_edges)>0:
+            return selected_edges

pyTEMlib/xrpa_x_sections.py

@@ -387,31 +387,45 @@ x_sections = {'1': {'name': 'H',
         5.849270e+04, 6.252870e+04, 6.684318e+04, 7.145536e+04,
         7.638578e+04, 8.165640e+04, 8.729069e+04, 9.331374e+04,
         9.975239e+04]),
-                    'dat': np.array([1.73384709e+17, 1.68319106e+17, 4.17741709e+16, 3.70675760e+16,
-                                     3.27899957e+16, 2.89145043e+16, 2.83239362e+16, 2.75089880e+16,
-                                     2.72971733e+16, 3.39872874e+16, 3.34739059e+16, 3.29533443e+16,
-                                     3.11062482e+16, 2.96127749e+16, 2.82646998e+16, 2.69920165e+16,
-                                     2.57318984e+16, 2.44484448e+16, 2.31237053e+16, 2.17576798e+16,
-                                     2.03593437e+16, 1.89430571e+16, 1.75265911e+16, 1.61291524e+16,
-                                     1.47677941e+16, 1.34574149e+16, 1.22096826e+16, 1.10330339e+16,
-                                     9.93339235e+15, 8.91327112e+15, 7.97374718e+15, 7.11320501e+15,
-                                     6.32841352e+15, 5.61416710e+15, 4.96741419e+15, 4.38492371e+15,
-                                     3.86202856e+15, 3.39477965e+15, 2.97833037e+15, 2.60639808e+15,
-                                     2.27431568e+15, 1.98172416e+15, 1.72431542e+15, 1.49840964e+15,
-                                     1.30047058e+15, 1.12735692e+15, 9.76196603e+14, 8.44404766e+14,
-                                     7.29665810e+14, 6.29933387e+14, 5.70768869e+14, 5.51849147e+14,
-                                     5.46948688e+14, 1.46983260e+16, 1.46076765e+16, 1.41693277e+16,
-                                     1.28133545e+16, 1.11570711e+16, 9.66072578e+15, 8.32072842e+15,
-                                     7.13187342e+15, 6.08769866e+15, 5.17833139e+15, 4.39138586e+15,
-                                     3.71429677e+15, 3.13413984e+15, 2.63906781e+15, 2.21795142e+15,
-                                     1.86073846e+15, 1.55866913e+15, 1.30370165e+15, 1.08892512e+15,
-                                     9.08362042e+14, 7.56788864e+14, 6.29753883e+14, 5.23451614e+14,
-                                     4.34597134e+14, 3.60372230e+14, 2.98515152e+14, 2.47051355e+14,
-                                     2.04347354e+14, 1.67545444e+14, 1.37356461e+14, 1.12606449e+14,
-                                     9.23153171e+13, 7.56824765e+13, 6.20455576e+13, 5.08660485e+13,
-                                     4.17005742e+13, 3.41865368e+13, 2.80277546e+13, 2.29783070e+13,
-                                     1.88371498e+13, 1.54434471e+13, 1.26607761e+13, 1.03796393e+13,
-                                     8.50956662e+12])},
+                    'dat': np.array([0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.73384709E+17, 
+       1.68319106E+17, 4.17741709E+16, 3.70675760E+16, 3.27899957E+16, 
+       2.89145043E+16, 2.83239362E+16, 2.75089880E+16, 2.72971733E+16, 
+       3.39872874E+16, 3.34739059E+16, 3.29533443E+16, 3.11062482E+16,
+       2.96127749E+16, 2.82646998E+16, 2.69920165E+16, 2.57318984E+16,
+       2.44484448E+16, 2.31237053E+16, 2.17576798E+16, 2.03593437E+16,
+       1.89430571E+16, 1.75265911E+16, 1.61291524E+16, 1.47677941E+16,
+       1.34574149E+16, 1.22096826E+16, 1.10330339E+16, 9.93339235E+15,
+       8.91327112E+15, 7.97374718E+15, 7.11320501E+15, 6.32841352E+15, 
+       5.61416710E+15, 4.96741419E+15, 4.38492371E+15, 3.86202856E+15, 
+       3.39477965E+15, 2.97833037E+15, 2.60639808E+15, 2.27431568E+15,
+       1.98172416E+15, 1.72436928E+15, 1.49846349E+15, 1.30052443E+15,
+       1.12741077E+15, 9.76268405E+14, 8.44476568E+14, 7.29737611E+14,
+       6.30005189E+14, 5.70840670E+14, 5.51938899E+14, 5.47038440E+14,
+       1.46983260E+16, 1.46076765E+16, 1.41693277E+16, 1.28133545E+16,
+       1.11572506E+16, 9.66090528E+15, 8.32090792E+15, 7.13205293E+15,
+       6.08787816E+15, 5.17851090E+15, 4.39156536E+15, 3.71447627E+15,
+       3.13431934E+15, 2.63924731E+15, 2.21813093E+15, 1.86091797E+15,
+       1.55881274E+15, 1.30384525E+15, 1.08906872E+15, 9.08505645E+14,
+       7.56932467E+14, 6.29897486E+14, 5.23595218E+14, 4.34740738E+14, 
+       3.60515834E+14, 2.98658755E+14, 2.47194958E+14, 2.04490957E+14,
+       1.67685457E+14, 1.37494679E+14, 1.12742872E+14, 9.24481501E+13,
+       7.58135144E+13, 6.21730054E+13, 5.09917013E+13, 4.18226370E+13,
+       3.43050094E+13, 2.81426371E+13, 2.30895995E+13, 1.89448522E+13,
+       1.55477390E+13, 1.27614779E+13, 1.04767510E+13, 8.60308821E+12,
+       7.03727482E+12, 5.73622982E+12, 4.67554069E+12, 3.79453506E+12,
+       3.08136566E+12, 2.50408080E+12, 2.03665238E+12, 1.65802460E+12,
+       1.35144972E+12, 1.10312388E+12, 9.01863997E+11, 7.38641010E+11,
+       6.06292710E+11, 4.99021120E+11, 4.11979630E+11, 3.41362757E+11,
+       2.83688122E+11, 2.35922107E+11, 1.97382598E+11, 1.66220704E+11,
+       1.41029113E+11, 1.20641048E+11, 1.04123090E+11, 9.07249117E+10,
+       7.98397891E+10, 7.09812667E+10, 6.37616158E+10, 5.78595243E+10,
+       5.30236866E+10, 4.90476730E+10, 4.57681349E+10, 4.30468542E+10,
+       4.07797187E+10, 3.88626160E+10, 3.72434899E+10, 3.58648992E+10,
+       3.46819678E+10, 3.36534099E+10, 3.27487098E+10, 3.19445318E+10,
+       3.12157456E+10, 3.05515808E+10, 2.99358821E+10, 2.93578792E+10, 
+       2.88103920E+10, 2.82844453E+10, 2.77764490E+10, 2.72810179E+10, 
+       2.67963571E+10, 2.63170814E+10, 2.58449859E+10, 2.53746854E+10, 
+       2.49061800E+10,])},
               '6': {'name': 'C',
                     'barns': 199447000000.0,
                     'NumEdges': 3,

{pyTEMlib-0.2023.3.0.dist-info → pyTEMlib-0.2023.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyTEMlib
-Version: 0.2023.3.0
+Version: 0.2023.8.0
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
 Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
 Author: Gerd Duscher
@@ -18,7 +18,6 @@ Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
@@ -34,12 +33,13 @@ Requires-Dist: plotly
 Requires-Dist: pandas
 Requires-Dist: requests
 Requires-Dist: lxml
+Requires-Dist: ipympl
 Requires-Dist: spglib
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: pyNSID (>=0.0.7)
-Requires-Dist: sidpy (>=0.11.2)
-Requires-Dist: SciFiReaders (>=0.0.8)
+Requires-Dist: pyNSID >=0.0.7
+Requires-Dist: sidpy >=0.11.2
+Requires-Dist: SciFiReaders >=0.0.8
 
 pyTEMlib
 ========

pyTEMlib-0.2023.8.0.dist-info/RECORD

@@ -0,0 +1,40 @@
+pyTEMlib/__init__.py,sha256=nEN93amIEoZxO7rJgN71ABeCoXrnmaywBbE97l5lPio,178
+pyTEMlib/animation.py,sha256=oPxbTuy8LfdH2mOOgm9Q40ArFAJmXM_58UV97ptcNAY,25187
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 Tag: py3-none-any

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