torch dev for ring_cnn + 2p spatial

Author: mannypaeza

caiman/source_extraction/cnmf/online_cnmf.py

@@ -323,9 +323,9 @@ def _prepare_object(self, Yr, T, new_dims=None, idx_components=None):
         if self.params.get('online', 'path_to_model') is None or self.params.get('online', 'sniper_mode') is False:
             loaded_model = None
             self.params.set('online', {'sniper_mode': False})
-            # self.tf_in = None
-            # self.tf_out = None
-            self.use_torch = None #fix 
+            self.tf_in = None
+            self.tf_out = None
+            # self.use_torch = None 
         else:
             try: 
                 from keras.models import load_model 
@@ -340,12 +340,12 @@ def _prepare_object(self, Yr, T, new_dims=None, idx_components=None):
                 # uses online model -> be careful 
                 model_path = ".".join(path + ["keras"])
                 loaded_model = model_load(model_path)
-                self.use_torch = False 
+                # self.use_torch = False 
             else: 
                 model_path = '.'.join(path + ['pt'])
                 loaded_model = load_graph(model_path)
                 loaded_model = torch.load(model_file)
-                self.use_torch = True 
+                # self.use_torch = True 
 
         self.loaded_model = loaded_model
 
@@ -547,8 +547,8 @@ def fit_next(self, t, frame_in, num_iters_hals=3):
                 sniper_mode=self.params.get('online', 'sniper_mode'),
                 use_peak_max=self.params.get('online', 'use_peak_max'),
                 mean_buff=self.estimates.mean_buff,
-                # tf_in=self.tf_in, tf_out=self.tf_out,
-                use_torch=self.use_torch,
+                tf_in=self.tf_in, tf_out=self.tf_out,
+                # use_torch=self.use_torch,
                 ssub_B=ssub_B, W=self.estimates.W if self.is1p else None,
                 b0=self.estimates.b0 if self.is1p else None,
                 corr_img=self.estimates.corr_img if use_corr else None,
@@ -2003,8 +2003,8 @@ def get_candidate_components(sv, dims, Yres_buf, min_num_trial=3, gSig=(5, 5),
                              patch_size=50, loaded_model=None, test_both=False,
                              thresh_CNN_noisy=0.5, use_peak_max=False,
                              thresh_std_peak_resid = 1, mean_buff=None,
-                             # tf_in=None, tf_out=None):
-                             use_torch=None):
+                             tf_in=None, tf_out=None):
+                             # use_torch=None):
     """
     Extract new candidate components from the residual buffer and test them
     using space correlation or the CNN classifier. The function runs the CNN
@@ -2146,8 +2146,8 @@ def update_num_components(t, sv, Ab, Cf, Yres_buf, Y_buf, rho_buf,
                           corr_img=None, first_moment=None, second_moment=None,
                           crosscorr=None, col_ind=None, row_ind=None, corr_img_mode=None,
                           max_img=None, downscale_matrix=None, upscale_matrix=None,
-                          # tf_in=None, tf_out=None):
-                          torch_in=None, torch_out=None):
+                          tf_in=None, tf_out=None):
+                          # torch_in=None, torch_out=None):
     """
     Checks for new components in the residual buffer and incorporates them if they pass the acceptance tests
     """
@@ -2177,8 +2177,8 @@ def update_num_components(t, sv, Ab, Cf, Yres_buf, Y_buf, rho_buf,
         sniper_mode=sniper_mode, rval_thr=rval_thr, patch_size=50,
         loaded_model=loaded_model, thresh_CNN_noisy=thresh_CNN_noisy,
         use_peak_max=use_peak_max, test_both=test_both, mean_buff=mean_buff,
-        # tf_in=tf_in, tf_out=tf_out)
-        torch_in=torch_in, torch_out=torch_out)
+        tf_in=tf_in, tf_out=tf_out)
+        #torch_in=torch_in, torch_out=torch_out)
 
     ind_new_all = ijsig_all
 

caiman/utils/nn_models.py

@@ -555,7 +555,7 @@ def fit_NL_model(model_NL, Y, patience=5, val_split=0.2, batch_size=32,
         Y = np.expand_dims(Y, axis=-1)
     run_logdir = get_run_logdir()
     os.mkdir(run_logdir)
-    path_to_model = os.path.join(run_logdir, 'model.h5')
+    path_to_model = os.path.join(run_logdir, 'model.weights.h5')
     chk = ModelCheckpoint(filepath=path_to_model,
                           verbose=0, save_best_only=True, save_weights_only=True)
     es = EarlyStopping(monitor='val_loss', patience=patience,
@@ -566,7 +566,7 @@ def fit_NL_model(model_NL, Y, patience=5, val_split=0.2, batch_size=32,
     history_NL = model_NL.fit(Y, Y, epochs=epochs, batch_size=batch_size,
                             shuffle=True, validation_split=val_split,
                             callbacks=callbacks)
-    model_NL.load_weights(os.path.join(run_logdir, 'model.h5'))
+    model_NL.load_weights(os.path.join(run_logdir, 'model.weights.h5'))
     return model_NL, history_NL, path_to_model
 
 def get_MCNN_model(Y, gSig=5, n_channels=8, lr=1e-4, pct=10, r_factor=1.5,