Merge pull request #183 from pycroscopy/use_dict3

infoWidget with plotly

Author: gduscher

notebooks/0_pyTEMlib.ipynb

@@ -63,7 +63,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.13.0"
   },
   "toc": {
    "base_numbering": "1",

notebooks/Spectroscopy/Analyse_Low_Loss.ipynb

@@ -191,14 +191,16 @@ def update_cl_sidebar(self):
                     cl_index = index+1
         self.core_loss_tab[0, 0].options = spectrum_list
         self.core_loss_tab[0, 0].value = spectrum_list[cl_index]
-        self.update_cl_dataset()
-        self.set_fit_start()
-        self.parent.plot()
+        if '_relationship' in self.parent.datasets.keys():
+            self.update_cl_dataset()
+            self.set_fit_start()
+            self.parent.plot()
 
     def update_cl_dataset(self, value=0):
         self.cl_key = self.core_loss_tab[0, 0].value.split(':')[0]
         self.parent.coreloss_key = self.cl_key
-        self.parent.datasets['_relationship']['core_loss'] = self.cl_key
+        if '_relationship' in self.parent.datasets.keys():
+            self.parent.datasets['_relationship']['core_loss'] = self.cl_key
 
         if 'None' in self.cl_key:
             return

notebooks/Spectroscopy/EDS.ipynb

@@ -395,6 +395,15 @@ def align_zero_loss(dataset: sidpy.Dataset) -> sidpy.Dataset:
     new_si.metadata.update({'zero_loss': {'shifted': shifts}})
     return new_si
 
+from numba import jit
+
+def get_zero_losses(energy, z_loss_params):
+    z_loss_dset = np.zeros((z_loss_params.shape[0], z_loss_params.shape[1], energy.shape[0]))
+    for x in range(z_loss_params.shape[0]):
+        for y in range(z_loss_params.shape[1]):
+            z_loss_dset[x, y] +=  zl_func(energy, *z_loss_params[x, y])
+    return z_loss_dset
+
 
 
 
@@ -488,11 +497,12 @@ def guess_function(xvec, yvec):
     z_loss_dset = dataset.copy()
     z_loss_dset *= 0.0
 
-    energy_grid = np.broadcast_to(energy.reshape((1, 1, -1)), (z_loss_dset.shape[0],
-                                                               z_loss_dset.shape[1], energy.shape[0]))
-    z_loss_peaks = zl_func(energy_grid, *z_loss_params)
-    z_loss_dset += z_loss_peaks
-
+    #energy_grid = np.broadcast_to(energy.reshape((1, 1, -1)), (z_loss_dset.shape[0],
+    #                                                           z_loss_dset.shape[1], energy.shape[0]))
+    #z_loss_peaks = zl_func(energy_grid, *z_loss_params)
+    z_loss_params = np.array(z_loss_params)
+    z_loss_dset += get_zero_losses(np.array(energy), np.array(z_loss_params))
+    
     shifts = z_loss_params[:, :, 0] * z_loss_params[:, :, 3]
     widths = z_loss_params[:, :, 2] * z_loss_params[:, :, 5]
 
@@ -522,7 +532,15 @@ def drude_lorentz(eps_inf, leng, ep, eb, gamma, e, amplitude):
     return eps
 
 
-def fit_plasmon(dataset: Union[sidpy.Dataset, np.ndarray], startFitEnergy: float, endFitEnergy: float, plot_result: bool = False, number_workers: int = 4, number_threads: int = 8) -> Union[sidpy.Dataset, np.ndarray]:
+def get_plasmon_losses(energy, params):
+    dset = np.zeros((params.shape[0], params.shape[1], energy.shape[0]))
+    for x in range(params.shape[0]):
+        for y in range(params.shape[1]):
+            dset[x, y] +=  energy_loss_function(energy, params[x, y])
+    return dset
+
+
+def fit_plasmon(dataset: Union[sidpy.Dataset, np.ndarray], startFitEnergy: float, endFitEnergy: float,  number_workers: int = 4, number_threads: int = 8) -> Union[sidpy.Dataset, np.ndarray]:
     """
     Fit plasmon peak positions and widths in a TEM dataset using a Drude model.
 
@@ -567,8 +585,6 @@ def energy_loss_function(E: np.ndarray, Ep: float, Ew: float, A: float) -> np.nd
         elf = (-1/eps).imag  
         return A*elf
 
-
-
     # define window for fitting
     energy = dataset.get_spectral_dims(return_axis=True)[0].values
     start_fit_pixel = np.searchsorted(energy, startFitEnergy)
@@ -589,37 +605,46 @@ def energy_loss_function(E: np.ndarray, Ep: float, Ew: float, A: float) -> np.nd
         guess_pos = energy[guess_pos]
         if guess_width >8:
             guess_width=8
-        popt, pcov = curve_fit(energy_loss_function, energy[start_fit_pixel:end_fit_pixel], fit_dset,
-                               p0=[guess_pos, guess_width, guess_amplitude])
+        try:
+            popt, pcov = curve_fit(energy_loss_function, energy[start_fit_pixel:end_fit_pixel], fit_dset,
+                                p0=[guess_pos, guess_width, guess_amplitude])
+        except:
+            end_fit_pixel = np.searchsorted(energy, 30)
+            fit_dset = np.array(dataset[start_fit_pixel:end_fit_pixel]/ anglog[start_fit_pixel:end_fit_pixel])
+            try:
+                popt, pcov = curve_fit(energy_loss_function, energy[start_fit_pixel:end_fit_pixel], fit_dset,
+                                p0=[guess_pos, guess_width, guess_amplitude])
+            except:
+                popt=[0,0,0]
 
         plasmon = dataset.like_data(energy_loss_function(energy, popt[0], popt[1], popt[2]))
         plasmon *= anglog
         start_plasmon = np.searchsorted(energy, 0)+1
-        
-        
         plasmon[:start_plasmon] = 0.
+        
         epsilon = drude(energy, popt[0], popt[1], 1) * popt[2]
         epsilon[:start_plasmon] = 0.
-
+        
         plasmon.metadata['plasmon'] = {'parameter': popt, 'epsilon':epsilon}
         return plasmon
 
     # if it can be parallelized:
     fitter = SidFitter(fit_dset, energy_loss_function, num_workers=number_workers,
                        threads=number_threads, return_cov=False, return_fit=False, return_std=False,
                        km_guess=False, num_fit_parms=3)
-    [fitted_dataset] = fitter.do_fit()
+    [fit_parameter] = fitter.do_fit()
+
+    plasmon_dset = dataset * 0.0
+    fit_parameter = np.array(fit_parameter)
+    plasmon_dset += get_plasmon_losses(np.array(energy), fit_parameter)
+    if 'plasmon' not in plasmon_dset.metadata:
+        plasmon_dset.metadata['plasmon'] = {}
+    plasmon_dset.metadata['plasmon'].update({'startFitEnergy': startFitEnergy,
+                                              'endFitEnergy': endFitEnergy,
+                                              'fit_parameter': fit_parameter,
+                                              'original_low_loss': dataset.title})
 
-    if plot_result:
-        fig, (ax1, ax2, ax3) = plt.subplots(1, 3, sharex=True, sharey=True)
-        ax1.imshow(fitted_dataset[:, :, 0], cmap='jet')
-        ax1.set_title('Ep - Peak Position')
-        ax2.imshow(fitted_dataset[:, :, 1], cmap='jet')
-        ax2.set_title('Ew - Peak Width')
-        ax3.imshow(fitted_dataset[:, :, 2], cmap='jet')
-        ax3.set_title('A - Amplitude')
-        plt.show()
-    return fitted_dataset
+    return plasmon_dset
 
 
 def angle_correction(spectrum):
@@ -722,8 +747,11 @@ def multiple_scattering(energy_scale: np.ndarray, p: list, core_loss=False)-> np
         ssd = ssd * ssd2
 
     PSD /=tmfp*np.exp(-tmfp)
-    BGDcoef = scipy.interpolate.splrep(LLene, PSD, s=0)    
-    return scipy.interpolate.splev(energy_scale, BGDcoef)
+    BGDcoef = scipy.interpolate.splrep(LLene, PSD, s=0)   
+    msd = scipy.interpolate.splev(energy_scale, BGDcoef)
+    start_plasmon = np.searchsorted(energy_scale, 0)+1
+    msd[:start_plasmon] = 0. 
+    return msd
 
 def fit_multiple_scattering(dataset: Union[sidpy.Dataset, np.ndarray], startFitEnergy: float, endFitEnergy: float,pin=None, number_workers: int = 4, number_threads: int = 8) -> Union[sidpy.Dataset, np.ndarray]:
     """

pyTEMlib/core_loss_widget.py

@@ -787,6 +787,55 @@ def h5_group_to_dict(group, group_dict={}):
     return group_dict
 
 
+def read_annotation(image):
+    if 'MAGE' not in image.data_type.name:
+        return {}
+    scale_x = np.abs(image.x[1]-image.x[0])
+    scale_y = np.abs(image.y[1]-image.y[0])
+    rec_scale = np.array([scale_x, scale_y,scale_x, scale_y])
+    if 'DocumentObjectList' not in image.original_metadata:
+        return {}
+    if '0' not in image.original_metadata['DocumentObjectList']:
+        return {}
+    annotations = {}        
+    tags = image.original_metadata['DocumentObjectList']['0']     
+    for key in tags:
+        if 'AnnotationGroupList' in key:
+            an_tags = tags[key]
+            for key2 in an_tags:
+                if isinstance(an_tags[key2], dict):
+                    if an_tags[key2]['AnnotationType'] == 13:  #type 'text'
+                        annotations[key2] = {'type': 'text'}
+                        if 'Label' in an_tags:
+                            annotations[key2]['label'] = an_tags['Label']
+                        rect = np.array(an_tags[key2]['Rectangle']) * rec_scale
+                        annotations[key2]['position'] = [rect[1],rect[0]]
+                        annotations[key2]['text'] = an_tags['Text'] 
+                        
+                    elif an_tags[key2]['AnnotationType']==6:
+                        annotations[key2] = {'type': 'circle'}
+                        if 'Label' in an_tags:
+                            annotations[key2]['label'] = an_tags['Label']
+                        rect = np.array(an_tags[key2]['Rectangle']) * rec_scale
+                    
+                        annotations[key2]['radius'] =rect[3]-rect[1]
+                        annotations[key2]['position'] = [rect[1],rect[0]]
+        
+                    elif an_tags[key2]['AnnotationType'] == 23:
+                        annotations[key2] = {'type':  'spectral_image'}
+                        if 'Label' in an_tags[key2]:
+                            annotations[key2]['label'] = an_tags[key2]['Label']
+                        rect = np.array(an_tags[key2]['Rectangle']) * rec_scale
+                        
+                        annotations[key2]['width'] =rect[3]-rect[1]
+                        annotations[key2]['height'] =rect[2]-rect[0]
+                        annotations[key2]['position'] = [rect[1],rect[0]]
+                        annotations[key2]['Rectangle'] = np.array(an_tags[key2]['Rectangle'])
+    if len(annotations)>0:
+        image.metadata['annotations'] = annotations                
+    return annotations
+
+
 def open_file(filename=None,  h5_group=None, write_hdf_file=False, sum_frames=False):  # save_file=False,
     """Opens a file if the extension is .emd, .mrc, .hf5, .ndata, .dm3 or .dm4
 
@@ -850,11 +899,16 @@ def open_file(filename=None,  h5_group=None, write_hdf_file=False, sum_frames=Fa
                         dataset_dict[key] = h5_group_to_dict(master_group[key])
                 if not write_hdf_file:
                     file.close()
+            for dset in dataset_dict.values():
+                if isinstance(dset, sidpy.Dataset):
+                    if 'Measurement' in dset.title:
+                        dset.title = dset.title.split('/')[-1]
             return dataset_dict
     elif extension in ['.dm3', '.dm4', '.ndata', '.ndata1', '.h5', '.emd', '.emi', '.edaxh5', '.mrc']:
         # tags = open_file(filename)
         if extension in ['.dm3', '.dm4']:
             reader = SciFiReaders.DMReader(filename)
+
         elif extension in ['.emi']:
             try:
                 import hyperspy.api as hs
@@ -903,8 +957,10 @@ def open_file(filename=None,  h5_group=None, write_hdf_file=False, sum_frames=Fa
             if not isinstance(dset, dict):
                 print('Please use new SciFiReaders Package for full functionality')
             if isinstance(dset, sidpy.Dataset):
-                dset = [dset]
-            
+                dset = {'Channel_000': dset}
+            for key in dset:
+                read_annotation(dset[key])
+
         if isinstance(dset, dict):
             dataset_dict = dset