Merge pull request #33 from AminAlam/dev

multiple small bugs fixed

.gitignore

@@ -170,3 +170,5 @@ docs/source/_static
 docs/source/_templates
 docs/*.bat
 docs/Makefile
+
+paradigm.sh

elecphys/data_io.py

@@ -78,6 +78,7 @@ def load_all_npz_files(npz_folder: str, ignore_channels: [
         else:
             data, _ = load_npz(npz_file_path)
         data_all[ch_indx, :] = data
+        ch_indx += 1
     return data_all, fs
 
 
@@ -164,4 +165,4 @@ def write_separate_npz_files(
         Warning(f'{output_npz_folder} already exists. Files will be overwritten.')
     for ch_indx in range(data.shape[0]):
         np.savez(os.path.join(output_npz_folder,
-                 f'Ch{ch_indx}.npz'), data=data[ch_indx, :], fs=fs)
+                 f'Ch{ch_indx+1}.npz'), data=data[ch_indx, :], fs=fs)

elecphys/preprocessing.py

@@ -191,9 +191,7 @@ def re_reference(data: np.ndarray, ignore_channels: [
         channels_list = [i for i in range(data.shape[0])]
 
     rr_channel = rr_channel - 1 if rr_channel is not None else None
-
     data_rereferenced = data.copy()
-
     if rr_channel is not None:
         reference = data[rr_channel, :].reshape(1, -1)
         data_rereferenced[channels_list, :] = data[channels_list,
@@ -202,5 +200,4 @@ def re_reference(data: np.ndarray, ignore_channels: [
         reference = np.mean(data[channels_list, :], axis=0).reshape(1, -1)
         data_rereferenced[channels_list, :] = data[channels_list,
                                                    :] - np.repeat(reference, len(channels_list), axis=0)
-
     return data_rereferenced

elecphys/utils.py

@@ -36,6 +36,7 @@ def sort_file_names(file_names: list) -> list:
         file_names: list
             sorted list of file names
     """
+    file_names = keep_npz_files(file_names)
     file_names_with_number = []
     file_names_without_number = []
     for file_name in file_names:

elecphys/visualization.py

@@ -183,6 +183,7 @@ def plot_stft_from_array(Zxx: np.ndarray, t: np.ndarray, f: np.ndarray, f_min: i
     f = f[desired_freq_index_low:desired_freq_index_high]
     t = t[desired_time_index_low:desired_time_index_high]
 
+    plt.figure(figsize=(30, 15))
     pc = plt.pcolormesh(t, f, Zxx, cmap=plt.get_cmap('jet'), shading='auto')
     plt.colorbar(pc)
     plt.xlabel('Time (s)')
@@ -234,6 +235,7 @@ def plot_signals_from_npz(npz_folder_path: str, output_plot_file: str, t_min: fl
     """
 
     npz_files = os.listdir(npz_folder_path)
+    # remove non-NPZ files
     npz_files = utils.sort_file_names(npz_files)
 
     if channels_list is None:
@@ -308,6 +310,8 @@ def plot_signals_from_npz(npz_folder_path: str, output_plot_file: str, t_min: fl
             ax[row_no].tick_params(axis='both', which='both', length=0)
             ax[row_no].set_yticks([])
             ax[row_no].set_xlim(t_min, t_max)
+            if row_no != len(channels_list) - 1:
+                ax[row_no].set_xticks([])
         else:
             scale_bar_size = np.max(signal_chan) - np.min(signal_chan)
             ax[row_no, 0].plot(t, signal_chan, color='k')
@@ -325,8 +329,9 @@ def plot_signals_from_npz(npz_folder_path: str, output_plot_file: str, t_min: fl
                 1 / fs, 0, f'{scale_bar_size:.2f} uV', ha='left')
             ax[row_no, 1].axis('off')
             ax[row_no, 0].set_xlim(t_min, t_max)
-            ax[row_no, 0].set_xticks([])
-            ax[row_no, 1].set_xticks([])
+            if row_no != len(channels_list) - 1:
+                ax[row_no, 0].set_xticks([])
+                ax[row_no, 1].set_xticks([])
 
     if not scale_bar:
         ax[-1].set_xlabel('Time (s)')

setup.py

@@ -26,7 +26,7 @@ def read_description():
 
 setup(
     name="ElecPhys",
-    version="0.0.6",
+    version="0.0.53",
     author='Amin Alam',
     description='Electrophysiology data processing',
     long_description=read_description(),