pyTEMlib 0.2023.4.0__py2.py3-none-any.whl → 0.2023.8.0__py2.py3-none-any.whl

pyTEMlib/peak_dlg.py

@@ -14,7 +14,7 @@ try:
 
 except:
     Qt_available = False
-    print('Qt dialogs are not available')
+    # print('Qt dialogs are not available')
 
 
 if Qt_available:

pyTEMlib/version.py

@@ -1,6 +1,6 @@
 """
 version
 """
-_version = '0.2023.4.0'
+_version = '0.2023.8.0'
 __version__ = _version
-_time = '2023-04-01 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-0.2023.4.0.dist-info → pyTEMlib-0.2023.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyTEMlib
-Version: 0.2023.4.0
+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
+pyTEMlib/atom_tools.py,sha256=ViO4ZZZoCZ_Cp2KijiqKKOiQhGOWnye45T0rsiPhf4I,7314
+pyTEMlib/config_dir.py,sha256=NWAseETgFNfBgHfBFv7ZTl7RsFzrLdGlhTN5Bn5FrTg,2104
+pyTEMlib/crystal_tools.py,sha256=KGW_fQqr2L8iJnGh31gi6qbJOeHt-Y7mOeIHx_Psxb8,61676
+pyTEMlib/diffraction_plot.py,sha256=pM5d3bdBGa8LlPZ5lw8sLT94mlYTXELxPLv-jUP2FWY,27959
+pyTEMlib/dynamic_scattering.py,sha256=O9MxnxfndWJ2VhQRjksKNQ4yY7y-gN_hitRQ4Qox4ns,9472
+pyTEMlib/eds_tools.py,sha256=gPrKT3U8lS7V36Njk72CWI-ovsoFv-EvwB8U9zBhpGU,3546
+pyTEMlib/eels_dialog.py,sha256=IuiekHXOz7kL36TGv3dJAunifSiMF-92U-s9PrSAqTo,61225
+pyTEMlib/eels_dialog_utilities.py,sha256=hCNIu5UcA1WZtsFMNw3go_kzYgm2nGjvwxDKhLFZpxg,54612
+pyTEMlib/eels_dlg.py,sha256=t3DotxKBqgmqUd_ITQGfzdDWaHANj5CYsHt4hc8chSY,9834
+pyTEMlib/eels_tools.py,sha256=n6ke9XEqvzMXYrri0EmIE9pJ2sZZdV55Dolton9-Gvg,75435
+pyTEMlib/file_tools.py,sha256=wL50vVk7vwPKIua4-tCzjM_dAy5uWg0jUwLMv_BoTZI,46102
+pyTEMlib/file_tools_qt.py,sha256=tLZACS4JyGH_AOzNR_SGAhjA01y4VJB261opPhGMlm8,7223
+pyTEMlib/graph_tools.py,sha256=lXU0ty2kHv2aqJEHiTQliqkfLHWAELzBRIqEb7Ni6Nk,44148
+pyTEMlib/graph_viz.py,sha256=m5PwSn6l2r0bsaLWBDSHc9IGR3_PneG2BrZgnEdi07I,13644
+pyTEMlib/image_dialog.py,sha256=F-ZgKq7UnMtPPd1b9eqb7t8MXDfWN-8hVKwB2Il0x28,6235
+pyTEMlib/image_dlg.py,sha256=n5gradDiYOFGEQ3k_Wlk9RUYYzl4bl_hKLzNVcYteNE,5694
+pyTEMlib/image_tools.py,sha256=AqNdbiPvr0uRy_o89NiuuHjQQcdx-rhj90Ae7_aQGQs,37278
+pyTEMlib/info_dialog.py,sha256=E7kumPEzyEYumTcvV0sdYPjHM7MO2SAwcl9oT_nK_AA,32694
+pyTEMlib/info_dlg.py,sha256=A72cifLU12ucijP_Nxf2hsA8IUhIs5cKJ0yIbKRPjXk,9894
+pyTEMlib/info_widget.py,sha256=PcHQGx-Ndzdemt7XZ1nlb2aSGQYiC0ZZHx88B-nQkeI,32003
+pyTEMlib/interactive_eels.py,sha256=lzK6sgMTjoRyaUc48BgOgrG_xhuBqjXdp-kIeaTBVD0,912
+pyTEMlib/interactive_image.py,sha256=5PwypcA1OjLAD-fi8bmWWFHuOjdIPVY9Dh59V24WuDA,34
+pyTEMlib/kinematic_scattering.py,sha256=wuH0YvPz4PL3DksPNsRvkl6zsJP-Uy-QXGvLlwHxR6c,61071
+pyTEMlib/microscope.py,sha256=iigUF1UImHEfmL2wqEBBj3aNRgEYouDbIln8VCo4_KM,1545
+pyTEMlib/peak_dialog.py,sha256=dBJshnBcmtn8L2BJpTclshTukJYXYbd0dFJEJmbyCjU,56368
+pyTEMlib/peak_dlg.py,sha256=qcjcnhwpGa4jBCeXzwQz9sCyX-tHsLLQ67ToqfKOiQY,11550
+pyTEMlib/probe_tools.py,sha256=8tPQuANClLsGAKnZo6Vo4gNIGKfyDR6WUMO3dXcm_4k,27177
+pyTEMlib/sidpy_tools.py,sha256=0oIx-qMtEmcZmLazQKW19dd-KoxyY3B15aIeMcyHA8E,4878
+pyTEMlib/simulation_tools.py,sha256=RmegD5TpQMU68uASvzZWVplAqs7bM5KkF6bWDWLjyc0,2799
+pyTEMlib/version.py,sha256=L6feq1ILXLEf4Sl5r76W5rml6QzybDbUuBsZS947eYE,93
+pyTEMlib/viz.py,sha256=Z36r4OptraJVIQlZx57_1wwwrwnxWVZyNoCOjeNj_ac,18439
+pyTEMlib/xrpa_x_sections.py,sha256=WeR7dc6SjYukk1S_8kR6IQFDqPagETTMJkFmbP78OPU,1805870
+pyTEMlib-0.2023.8.0.dist-info/LICENSE,sha256=ASQTnQgYv39esmSFeb-IDhPwOMZSqGJ4s19vy4YtIaA,1069
+pyTEMlib-0.2023.8.0.dist-info/METADATA,sha256=6fqx1QSoxo3E-0CvA6NB70ukueyAefT0Z1YVnGpz2u8,3280
+pyTEMlib-0.2023.8.0.dist-info/WHEEL,sha256=m9WAupmBd2JGDsXWQGJgMGXIWbQY3F5c2xBJbBhq0nY,110
+pyTEMlib-0.2023.8.0.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
+pyTEMlib-0.2023.8.0.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
+pyTEMlib-0.2023.8.0.dist-info/RECORD,,

{pyTEMlib-0.2023.4.0.dist-info → pyTEMlib-0.2023.8.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: bdist_wheel (0.41.1)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

pyTEMlib-0.2023.4.0.dist-info/RECORD

@@ -1,39 +0,0 @@
-pyTEMlib/__init__.py,sha256=nEN93amIEoZxO7rJgN71ABeCoXrnmaywBbE97l5lPio,178
-pyTEMlib/animation.py,sha256=oPxbTuy8LfdH2mOOgm9Q40ArFAJmXM_58UV97ptcNAY,25187
-pyTEMlib/atom_tools.py,sha256=ViO4ZZZoCZ_Cp2KijiqKKOiQhGOWnye45T0rsiPhf4I,7314
-pyTEMlib/config_dir.py,sha256=NWAseETgFNfBgHfBFv7ZTl7RsFzrLdGlhTN5Bn5FrTg,2104
-pyTEMlib/crystal_tools.py,sha256=D8Di8uq1pBTZ8el9Pz48I8HgT6_fbqZCAh5A25ON5dw,59580
-pyTEMlib/diffraction_plot.py,sha256=pM5d3bdBGa8LlPZ5lw8sLT94mlYTXELxPLv-jUP2FWY,27959
-pyTEMlib/dynamic_scattering.py,sha256=O9MxnxfndWJ2VhQRjksKNQ4yY7y-gN_hitRQ4Qox4ns,9472
-pyTEMlib/eds_tools.py,sha256=gPrKT3U8lS7V36Njk72CWI-ovsoFv-EvwB8U9zBhpGU,3546
-pyTEMlib/eels_dialog.py,sha256=o680vo8tPHzLmr3pVW7nVNHioC3ENkEr6I5lMyoXtlw,32917
-pyTEMlib/eels_dialog_utilities.py,sha256=p52DIzLRN3f8-jW_hzoC5vvqb3OKB3qxYlc3DuHetMA,54546
-pyTEMlib/eels_dlg.py,sha256=3iH7CJGMrzcogKnl-Wd0I_X36tzGhw9al9oJG2Mq6xo,9762
-pyTEMlib/eels_tools.py,sha256=LOLevrp8DOlDdXzj4JOXZX_cGPS2Yyt0lfK3L44YDws,72938
-pyTEMlib/file_tools.py,sha256=fKXgNMeVKkG-DhZC-EG32O6wNn5SbXLR5foplwmKToQ,42516
-pyTEMlib/file_tools_qt.py,sha256=tLZACS4JyGH_AOzNR_SGAhjA01y4VJB261opPhGMlm8,7223
-pyTEMlib/graph_tools.py,sha256=aHd2Hff9zFHB5W5EvVsPwplLQMnqoRGddHIW0sJgeDY,16875
-pyTEMlib/graph_viz.py,sha256=m5PwSn6l2r0bsaLWBDSHc9IGR3_PneG2BrZgnEdi07I,13644
-pyTEMlib/image_dialog.py,sha256=EHlJG2MSwN_bw61TIdp6e_blYKTSQwUJKMxQcQyouWI,6233
-pyTEMlib/image_dlg.py,sha256=55eO-0ZOy144SopintvtNM4cRKFGU08lC0Gk6vwoV2A,5692
-pyTEMlib/image_tools.py,sha256=GwDqe0tzU6gym_Mi4bTdbcFoe96vH-OBIrsuwS24Enk,35797
-pyTEMlib/info_dialog.py,sha256=lfcoiHe9vvgj90TtjBdSPgcbcSTl2WKLEErzKEOo1LM,14394
-pyTEMlib/info_dlg.py,sha256=fsQXrANJ5GAqH_Glh9MhuI38Z4cfMDtNi2XgHbEyMB8,9892
-pyTEMlib/interactive_eels.py,sha256=i9TMHm5Ak_M6e4HKZNp4QQ2CPScNa5YpsoqfzSck-EA,645
-pyTEMlib/interactive_image.py,sha256=5PwypcA1OjLAD-fi8bmWWFHuOjdIPVY9Dh59V24WuDA,34
-pyTEMlib/kinematic_scattering.py,sha256=wuH0YvPz4PL3DksPNsRvkl6zsJP-Uy-QXGvLlwHxR6c,61071
-pyTEMlib/microscope.py,sha256=iigUF1UImHEfmL2wqEBBj3aNRgEYouDbIln8VCo4_KM,1545
-pyTEMlib/peak_dialog.py,sha256=z6SdlEfcTI473u4q2I4gUN5VVnJTfu27wQWTbOdeyRg,27881
-pyTEMlib/peak_dlg.py,sha256=2DeNDn6NVU1mK-HmdnQssAUNNWk35J31oRsYeBepi8o,11548
-pyTEMlib/probe_tools.py,sha256=8tPQuANClLsGAKnZo6Vo4gNIGKfyDR6WUMO3dXcm_4k,27177
-pyTEMlib/sidpy_tools.py,sha256=0oIx-qMtEmcZmLazQKW19dd-KoxyY3B15aIeMcyHA8E,4878
-pyTEMlib/simulation_tools.py,sha256=RmegD5TpQMU68uASvzZWVplAqs7bM5KkF6bWDWLjyc0,2799
-pyTEMlib/version.py,sha256=0j0pc3D1ED65TKRTO4GNA3z6nNv_mGvLI9ZOUX_uJss,93
-pyTEMlib/viz.py,sha256=0s4QCIWPq_z3WaXlAdQnH8QgeU1u3aoO3gCHWA0wSbE,9356
-pyTEMlib/xrpa_x_sections.py,sha256=WeR7dc6SjYukk1S_8kR6IQFDqPagETTMJkFmbP78OPU,1805870
-pyTEMlib-0.2023.4.0.dist-info/LICENSE,sha256=ASQTnQgYv39esmSFeb-IDhPwOMZSqGJ4s19vy4YtIaA,1069
-pyTEMlib-0.2023.4.0.dist-info/METADATA,sha256=_5-6MiujmmSKL6arzGGzaafYLQeA6ekiDBMjajTFLBE,3314
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