Fix bugs found by ai

djimaging/autorois/cellpose_wrapper.py

@@ -55,6 +55,8 @@ def create_mask_from_data(self, ch0_stack, ch1_stack=None, use_ch0=True, do_3D=F
 
         if isinstance(masks, list):
             if len(masks) == 0:
+                raise ValueError("Empty masks")
+            elif len(masks) == 1:
                 roi_mask = masks[0]
             else:
                 roi_mask = np.max(masks, axis=0)

djimaging/autorois/corr_roi_mask_utils.py

@@ -126,7 +126,7 @@ def corr_map_rois(stack, cut_x, cut_z, n_pix_max_x=5, n_pix_max_z=5, n_pix_max=2
         ignore_map[corr_map < line_threshold] = True
     ignore_map[:cut_x[0], :] = True
     ignore_map[nx - cut_x[1]:, :] = True
-    ignore_map[:, cut_z[0]] = True
+    ignore_map[:, :cut_z[0]] = True
     ignore_map[:, nz - cut_z[1]:] = True
 
     p_threshold = grow_threshold if grow_threshold is not None else line_threshold

djimaging/tables/core/experiment.py

@@ -152,7 +152,7 @@ def add_experiment(self, key, header_path, pre_data_dir, raw_data_dir, only_new,
             info_entry["prep"] = "wholemount"
 
         eye = header_dict.get("eye", "unknown")
-        if 'eye' == '':
+        if eye == '':
             eye = 'unknown'
 
         if (

djimaging/tables/receptivefield/rf_offset.py

@@ -73,7 +73,7 @@ def fetch_and_compute(self, key):
         """Compute offset w.r.t. stimulus center in microns"""
         stim_dict = (self.stimulus_tab & key).fetch1('stim_dict')
 
-        if ('pix_scale_x_um' not in stim_dict) or ('pix_scale_x_um' not in stim_dict):
+        if ('pix_scale_x_um' not in stim_dict) or ('pix_scale_y_um' not in stim_dict):
             raise ValueError("Pixel size not found in stimulus dict")
 
         pix_scale_x_um, pix_scale_y_um = stim_dict['pix_scale_x_um'], stim_dict['pix_scale_y_um']

djimaging/utils/receptive_fields/spatial_rf_utils.py

@@ -40,7 +40,7 @@ def fit_rf_model(srf, kind='gaussian', polarity=None, center=None):
     qi = -1.
 
     for polarity_i in polarities:
-        if kind == 'gauss':
+        if kind == 'gauss' or kind == 'gaussian':
             model_i = srf_gauss_model(srf, polarity=polarity_i, center=center)
         elif kind == 'dog':
             model_i = srf_dog_model(srf, polarity=polarity_i, center=center)
@@ -58,7 +58,7 @@ def fit_rf_model(srf, kind='gaussian', polarity=None, center=None):
         if qi_i > qi:
             model, model_fit, model_params, qi = model_i, model_i_fit, model_i_params, qi_i
 
-    if kind == 'gauss':
+    if kind == 'gauss' or kind == 'gaussian':
         return model_fit, model_params, qi
     elif kind == 'dog':
         model_c_fit = model[0](xx, yy)

djimaging/utils/receptive_fields/temporal_rf_utils.py

@@ -138,7 +138,7 @@ def compute_polarity_and_peak_idxs(trf, nstd=1., npeaks_max=None, rf_time=None,
     trf = trf.copy()
     std_trf = np.std(trf)
 
-    if (rf_time is not None) or (np.isfinite(max_dt_future)):
+    if (rf_time is not None) and (np.isfinite(max_dt_future)):
         trf[rf_time > max_dt_future] = 0.
 
     pos_peak_idxs, _ = find_peaks(trf, prominence=nstd * std_trf / 2., height=nstd * std_trf)

djimaging/utils/scanm/traces_and_triggers_utils.py

@@ -51,14 +51,20 @@ def compute_frame_times(n_frames: int, pix_dt: int, npix_x: int, npix_2nd: int,
     """Compute timepoints of frames and relative delay of individual pixels.
     npix_2nd can be npix_y (xy-scan) or npix_z (xz-scan)
     """
+    if npix_x_offset_left < 0:
+        raise ValueError(f"npix_x_offset_left has to be positive or 0, but was {npix_x_offset_left}")
+    if npix_x_offset_right < 0:
+        raise ValueError(f"npix_x_offset_right has to be positive or 0, but was {npix_x_offset_right}")
+
     frame_dt = pix_dt * npix_x * npix_2nd
 
     frame_dt_offset = (np.arange(npix_x * npix_2nd) * pix_dt).reshape(npix_2nd, npix_x).T
 
     if precision == 'line':
         frame_dt_offset = np.tile(frame_dt_offset[0, :], (npix_x, 1))
 
-    frame_dt_offset = frame_dt_offset[npix_x_offset_left:-npix_x_offset_right]
+    npix_x_offset_right_idx = npix_x_offset_left if npix_x_offset_left > 0 else None
+    frame_dt_offset = frame_dt_offset[npix_x_offset_left:-npix_x_offset_right_idx]
 
     frame_times = np.arange(n_frames) * frame_dt
 

djimaging/utils/scanm/wparams_utils.py

@@ -71,4 +71,4 @@ def check_dims_ch_stack_wparams(ch_stack, wparams):
     nzpix = wparams.get("user_dzpix", 0)
 
     if not (ch_stack.shape[:2] in [(nxpix, nypix), (nxpix, nzpix)]):
-        ValueError(f'Stack shape error: {ch_stack.shape} not in [{(nxpix, nypix)}, {(nxpix, nzpix)}]')
+        raise ValueError(f'Stack shape error: {ch_stack.shape} not in [{(nxpix, nypix)}, {(nxpix, nzpix)}]')