update

app.py

@@ -20,7 +20,7 @@ Upload your data's channel locations in `.loc` format, which can be obtained usi
 >If you cannot obtain it, we recommend you to download the standard montage <a href="">here</a>. If the channels in those files doesn't match yours, you can use **EEGLAB** to modify them to your needed montage.
 
 ## Mapping
-...
+(...)
 
 ### Step1: Mapping result
 After clicking the mapping button, the **template montage** and the **input montage** will be displayed, with the unmatched input channels highlighted in red.
@@ -41,7 +41,7 @@ There're two methods you can choose from:
 After filling all the template channels, you can then proceed to **run the model**.
 
 ## Run model
-...
+(...)
 
 """
 
@@ -67,7 +67,7 @@ init_js = """
 	    attribute = "name";
 	}else return;
 	
-	// add figure of in_montage
+	// add figure of mapped_montage
 	document.querySelector(selector).style.cssText = `
 		position: relative;
 		width: 560px;
@@ -99,8 +99,8 @@ init_js = """
 	left = channel_info.templateDict[channel].css_position[0];
 	bottom = channel_info.templateDict[channel].css_position[1];
 	
-	let rule = `
-		${selector}::after{
+	let dot_rule = `
+		${selector}::before{
 			content: '';
 			position: absolute;
 			background-color: red;
@@ -111,18 +111,32 @@ init_js = """
 			bottom: ${bottom};
 		}
 	`;
+	
+	left = parseFloat(left.slice(0, -1))+2.5
+	left = left.toString()+"%"
+	bottom = parseFloat(bottom.slice(0, -1))-1
+	bottom = bottom.toString()+"%"
+	let txt_rule = `
+		${selector}::after{
+			content: "${channel}";
+			position: absolute;
+			color: red;
+			left: ${left};
+			bottom: ${bottom};
+		}
+	`;
+	
 	// check if indicator already exist
-	let exist = 0;
 	const styleSheet = document.styleSheets[0];
 	for(let i=0; i<styleSheet.cssRules.length; i++){
-		if(styleSheet.cssRules[i].selectorText == selector+"::after"){
-			exist = 1;
-			//console.log('exist!');
+		let tmp = styleSheet.cssRules[i].selectorText;
+		if(tmp==selector+"::before" || tmp==selector+"::after"){
 			styleSheet.deleteRule(i);
-			styleSheet.insertRule(rule, styleSheet.cssRules.length);
+			i--;
 		}
 	}
-	if(exist == 0) styleSheet.insertRule(rule, styleSheet.cssRules.length);
+	styleSheet.insertRule(dot_rule, styleSheet.cssRules.length);
+	styleSheet.insertRule(txt_rule, styleSheet.cssRules.length);
 }
 """
 
@@ -162,9 +176,9 @@ update_js = """
 	left = channel_info.templateDict[channel].css_position[0];
 	bottom = channel_info.templateDict[channel].css_position[1];
 	
-	let rule = `
-		${selector}::after{
-			content: '';
+	let dot_rule = `
+		${selector}::before{
+			content: "";
 			position: absolute;
 			background-color: red;
 			width: 10px;
@@ -174,18 +188,33 @@ update_js = """
 			bottom: ${bottom};
 		}
 	`;
+	
+	left = parseFloat(left.slice(0, -1))+2.5
+	left = left.toString()+"%"
+	bottom = parseFloat(bottom.slice(0, -1))-1
+	bottom = bottom.toString()+"%"
+	let txt_rule = `
+		${selector}::after{
+			content: "${channel}";
+			position: absolute;
+			color: red;
+			left: ${left};
+			bottom: ${bottom};
+		}
+	`;
+	
 	// check if indicator already exist
-	let exist = 0;
 	const styleSheet = document.styleSheets[0];
 	for(let i=0; i<styleSheet.cssRules.length; i++){
-		if(styleSheet.cssRules[i].selectorText == selector+"::after"){
-			exist = 1;
-			//console.log('exist!');
+		let tmp = styleSheet.cssRules[i].selectorText;
+		if(tmp==selector+"::before" || tmp==selector+"::after"){
+			console.log('exist!!', tmp);
 			styleSheet.deleteRule(i);
-			styleSheet.insertRule(rule, styleSheet.cssRules.length);
+			i--;
 		}
 	}
-	if(exist == 0) styleSheet.insertRule(rule, styleSheet.cssRules.length);
+	styleSheet.insertRule(dot_rule, styleSheet.cssRules.length);
+	styleSheet.insertRule(txt_rule, styleSheet.cssRules.length);
 }
 """
 
@@ -198,7 +227,7 @@ with gr.Blocks() as demo:
 	with gr.Row():
 		gr.Markdown(
 			"""
-			<p style="text-align: center;">...</p>
+			<p style="text-align: center;">(...)</p>
 			"""
 		)
 	with gr.Row():
@@ -209,9 +238,9 @@ with gr.Blocks() as demo:
 			with gr.Row():
 				in_raw_data = gr.File(label="Raw data (.csv)", file_types=[".csv"])
 				in_raw_loc = gr.File(label="Channel locations (.loc, .locs)", file_types=[".loc", "locs"])
-				with gr.Column(): #min_width=100
-					in_samplerate = gr.Textbox(label="Sampling rate (Hz)")
-					map_btn = gr.Button("Mapping")
+			with gr.Row():
+				in_samplerate = gr.Textbox(label="Sampling rate (Hz)", scale=2)
+				map_btn = gr.Button("Mapping", scale=1)
 			
 			# ------------------------mapping------------------------
 			# description for stage1-123
@@ -220,11 +249,10 @@ with gr.Blocks() as demo:
 			# stage1-1 : mapping result
 			with gr.Row():
 				tpl_montage = gr.Image("./template_montage.png", label="Template montage", visible=False)
-				in_montage = gr.Image(elem_id="input-montage", label="Input channels", visible=False)
+				mapped_montage = gr.Image(elem_id="input-montage", label="Input channels", visible=False)
 			
 			# stage1-2 : assign unmatched input channels to empty template channels
-			radio = gr.Radio(elem_id="radio", visible=False) #, label=""
-			step2_btn = gr.Button("Next", visible=False) #, interactive=False
+			radio = gr.Radio(elem_id="radio", visible=False)
 			
 			# stage1-3 : select a way to fill the empty template channels
 			with gr.Row():
@@ -234,11 +262,13 @@ with gr.Blocks() as demo:
 									visible=False,
 									scale=2)
 				fillmode_btn = gr.Button("OK", visible=False, scale=1)
+			chkbox_group = gr.CheckboxGroup(elem_id="chkbox-group", visible=False)
 			
-			chkbox_group = gr.CheckboxGroup(elem_id="chkbox-group", label="", visible=False)
-			step3_btn = gr.Button("Next", visible=False)
-			next_btn = gr.Button("Next step", visible=False)
-			
+			with gr.Row():
+				clear_btn = gr.Button("Clear", visible=False) #, interactive=False
+				step2_btn = gr.Button("Next", visible=False)
+				step3_btn = gr.Button("Next", visible=False)
+				next_btn = gr.Button("Next step", visible=False)
 			# -------------------------------------------------------
 
 		with gr.Column():
@@ -249,7 +279,9 @@ with gr.Blocks() as demo:
 									("ART", "EEGART"),
 									("IC-U-Net", "ICUNet"),
 									("IC-U-Net++", "UNetpp"),
-									("IC-U-Net-Attn", "AttUnet")],
+									("IC-U-Net-Attn", "AttUnet"),
+									"(mapped data)",
+									"(denoised data)"],
 									value="EEGART",
 									label="Model",
 									scale=2)
@@ -279,7 +311,7 @@ with gr.Blocks() as demo:
     
 	#demo.load(js=js)
 	
-	# stage1
+	# -------------------------stage1: channel mapping-------------------------------
 	def reset_all(raw_data, raw_loc, samplerate):
 		# verify that all required inputs have been provided
 		if raw_data == None or raw_loc == None:
@@ -313,23 +345,25 @@ with gr.Blocks() as demo:
 		# reset layout
 		return {app_state_json : app_state,
 				channel_info_json : channel_info,
-				# ------------------Stage1-----------------------
+				# ------------------stage1-----------------------
 				desc_md : gr.Markdown("### Step1: Mapping result", visible=False),
 				tpl_montage : gr.Image(visible=False),
-				in_montage : gr.Image(value=None, visible=False),
+				mapped_montage : gr.Image(value=None, visible=False),
 				radio : gr.Radio(choices=[], value=[], label="", visible=False),
 				in_fill_mode : gr.Dropdown(value="mean", visible=False),
 				chkbox_group : gr.CheckboxGroup(choices=[], value=[], label="", visible=False),
-				fillmode_btn : gr.Button("OK", visible=False),
-				step2_btn : gr.Button("Next", visible=False),
-				step3_btn : gr.Button("Next", visible=False),
-				next_btn : gr.Button("Next step", visible=False),
-				# ------------------Stage2-----------------------
+				fillmode_btn : gr.Button(visible=False),
+				clear_btn : gr.Button(visible=False),
+				step2_btn : gr.Button(visible=False),
+				step3_btn : gr.Button(visible=False),
+				next_btn : gr.Button(visible=False),
+				# ------------------stage2-----------------------
 				run_btn : gr.Button(interactive=False),
 				batch_md : gr.Markdown(visible=False),
 				out_denoised_data : gr.File(visible=False)}
 	
-	# stage1-1
+	
+	# ---------------------------stage1-1-------------------------------
 	def mapping_result(app_state, channel_info, raw_loc):
 		filepath = app_state["filepath"]
 		filename1 = filepath+"raw_montage_"+str(random.randint(1,10000))+".png"
@@ -358,7 +392,7 @@ with gr.Blocks() as demo:
 		matched_num = 30 - len(app_state["missingTemplates"])
 		
 		# if the input channels(>=30) has all the 30 template channels
-		# -> Stage2.decode data
+		# -> stage2
 		if matched_num == 30:
 			app_state["stage1State"] = "finished"
 			gr.Info('The mapping process has been finished.')
@@ -366,7 +400,7 @@ with gr.Blocks() as demo:
 			return {app_state_json : app_state,
 					desc_md : gr.Markdown("### Mapping result", visible=True),
 					tpl_montage : gr.Image(visible=True),
-					in_montage : gr.Image(value=filename2, visible=True),
+					mapped_montage : gr.Image(value=filename2, visible=True),
 					run_btn : gr.Button(interactive=True)}
 		
 		# if matched channels < 30, and there're still some unmatched input channels
@@ -376,20 +410,20 @@ with gr.Blocks() as demo:
 		
 		# if input channels < 30, but all of them can match to some template channels
 		# -> directly use fill_mode to fill the remaining channels
-		if in_num == matched_num:
+		elif in_num == matched_num:
 			app_state["stage1State"] = "step3-initializing"
 		
 		return {app_state_json : app_state,
 				desc_md : gr.Markdown("### Step1: Mapping result", visible=True),
 				tpl_montage : gr.Image(visible=True),
-				in_montage : gr.Image(value=filename2, visible=True),
+				mapped_montage : gr.Image(value=filename2, visible=True),
 				next_btn : gr.Button("Next step", visible=True)}
 	
 	map_btn.click(
 	    fn = reset_all,
 	    inputs = [in_raw_data, in_raw_loc, in_samplerate],
-	    outputs = [app_state_json, channel_info_json, desc_md, tpl_montage, in_montage, radio, in_fill_mode,
-	               chkbox_group, fillmode_btn, step2_btn, step3_btn, next_btn, run_btn, batch_md, out_denoised_data]
+	    outputs = [app_state_json, channel_info_json, desc_md, tpl_montage, mapped_montage, radio, in_fill_mode, chkbox_group,
+	               fillmode_btn, clear_btn, step2_btn, step3_btn, next_btn, run_btn, batch_md, out_denoised_data]
 	).success(
 	    fn = mapping_stage1,
 	    inputs = [app_state_json, channel_info_json, in_raw_loc], 
@@ -398,7 +432,7 @@ with gr.Blocks() as demo:
 	).success(
 	    fn = mapping_result,
 	    inputs = [app_state_json, channel_info_json, in_raw_loc],
-	    outputs = [app_state_json, desc_md, tpl_montage, in_montage, next_btn, run_btn]
+	    outputs = [app_state_json, desc_md, tpl_montage, mapped_montage, next_btn, run_btn]
 	)
 	
 
@@ -423,16 +457,18 @@ with gr.Blocks() as demo:
 					    channel_info_json : channel_info,
 					    desc_md : gr.Markdown("### Step2: Assign unmatched input channels"),
 					    tpl_montage : gr.Image(visible=False),
-					    in_montage : gr.Image(visible=False),
+					    mapped_montage : gr.Image(visible=False),
 					    radio : gr.Radio(choices=app_state["stage1UnassignedInputs"], value=[], label=label, visible=True),
+					    clear_btn : gr.Button(visible=True),
 					    next_btn : gr.Button("Next step")}
 			else:
 			    return {app_state_json : app_state,
 					    channel_info_json : channel_info,
 					    desc_md : gr.Markdown("### Step2: Assign unmatched input channels"),
 					    tpl_montage : gr.Image(visible=False),
-					    in_montage : gr.Image(visible=False),
+					    mapped_montage : gr.Image(visible=False),
 					    radio : gr.Radio(choices=app_state["stage1UnassignedInputs"], value=[], label=label, visible=True),
+					    clear_btn : gr.Button(visible=True),
 					    step2_btn : gr.Button(visible=True),
 					    next_btn : gr.Button(visible=False)}
 		
@@ -450,7 +486,7 @@ with gr.Blocks() as demo:
 			        channel_info_json : channel_info,
 					desc_md : gr.Markdown("### Step3: Fill the remaining template channels"),
 					tpl_montage : gr.Image(visible=False),
-					in_montage : gr.Image(visible=False),
+					mapped_montage : gr.Image(visible=False),
 					in_fill_mode : gr.Dropdown(visible=True),
 					fillmode_btn : gr.Button(visible=True),
 					next_btn : gr.Button(visible=False)}
@@ -481,7 +517,7 @@ with gr.Blocks() as demo:
 			# if all the unmatched template channels were filled by input channels
 			# -> stage2
 			if len(app_state["missingTemplates"]) == 0:
-				print('step2 -> Stage2')
+				print('step2 -> stage2')
 				gr.Info('The mapping process has been finished.')
 				app_state["stage1State"] = "finished"
 				
@@ -489,6 +525,7 @@ with gr.Blocks() as demo:
 						channel_info_json : channel_info,
 						desc_md : gr.Markdown(visible=False),
 						radio : gr.Radio(visible=False),
+						clear_btn : gr.Button(visible=False),
 						next_btn : gr.Button(visible=False),
 						run_btn : gr.Button(interactive=True)}
 						
@@ -506,6 +543,7 @@ with gr.Blocks() as demo:
 						radio : gr.Radio(visible=False),
 						in_fill_mode : gr.Dropdown(visible=True),
 						fillmode_btn : gr.Button(visible=True),
+						clear_btn : gr.Button(visible=False),
 						next_btn : gr.Button(visible=False)}
 		
 		# stage1-3 -> stage2
@@ -523,7 +561,7 @@ with gr.Blocks() as demo:
 			
 			gr.Info('The mapping process has been finished.')
 			app_state["stage1State"] = "finished"
-			print('step3 -> Stage2')
+			print('step3 -> stage2')
 			
 			app_state["missingTemplates"] = [channel for channel in channel_info["templateOrder"]
 											if channel_info["templateDict"][channel]["matched"]==False]
@@ -537,8 +575,8 @@ with gr.Blocks() as demo:
 	next_btn.click(
 		fn = init_next_step,
 		inputs = [app_state_json, channel_info_json, radio, chkbox_group],
-		outputs = [app_state_json, channel_info_json, desc_md, tpl_montage, in_montage, radio, in_fill_mode,
-					chkbox_group, fillmode_btn, step2_btn, next_btn, run_btn]
+		outputs = [app_state_json, channel_info_json, desc_md, tpl_montage, mapped_montage, radio, in_fill_mode,
+					chkbox_group, fillmode_btn, clear_btn, step2_btn, next_btn, run_btn]
 	).success(
 	    fn = None,
 	    js = init_js,
@@ -546,8 +584,7 @@ with gr.Blocks() as demo:
 		outputs = []
 	)
 	
-	# stage1-2
-	# def update_selection()
+	# ---------------------------stage1-2-------------------------------
 	def update_radio(app_state, channel_info, selected):
 		
 		# save info before clicking on next_btn
@@ -594,7 +631,14 @@ with gr.Blocks() as demo:
 		outputs = []
 	)
 	
-	# stage1-3
+	clear_btn.click(
+	    fn = lambda : gr.Radio(value=[]),
+	    inputs = [],
+	    outputs = radio
+	)
+	
+	
+	# ---------------------------stage1-3-------------------------------
 	def fill_value(app_state, channel_info, fill_mode):
 		
 		if fill_mode == 'zero':
@@ -609,40 +653,31 @@ with gr.Blocks() as demo:
 		
 		elif fill_mode == 'mean':
 			app_state["stage1State"] = "step3-selecting"
-			app_state = find_neighbors(app_state, channel_info, fill_mode)
+			app_state = find_neighbors(app_state, channel_info)
 			
-			name = app_state["missingTemplates"][0]
-			idx = channel_info["templateDict"][name]["index"]
-			value = app_state["stage1NewOrder"][idx]
-			value = [channel_info["inputOrder"][i] for i in value]
-			label = name+' (1/'+str(app_state["totalFillingNum"])+')'
+			# init stage1-3-selecting
+			target_name = app_state["missingTemplates"][0]
+			target_idx = channel_info["templateDict"][target_name]["index"]
+			
+			chkbox_value = app_state["stage1NewOrder"][target_idx]
+			chkbox_value = [channel_info["inputOrder"][i] for i in chkbox_value]
+			chkbox_label = target_name+' (1/'+str(app_state["totalFillingNum"])+')'
 			
 			if app_state["totalFillingNum"] == 1:
 			    return {app_state_json : app_state,
 					    in_fill_mode : gr.Dropdown(visible=False),
 		        		fillmode_btn : gr.Button(visible=False),
 		        		chkbox_group : gr.CheckboxGroup(choices=channel_info["inputOrder"],
-													    value=value, label=label, visible=True),
+													    value=chkbox_value, label=chkbox_label, visible=True),
 		                next_btn : gr.Button(visible=True)}
 			else:
 			    return {app_state_json : app_state,
 					    in_fill_mode : gr.Dropdown(visible=False),
 		        		fillmode_btn : gr.Button(visible=False),
 		        		chkbox_group : gr.CheckboxGroup(choices=channel_info["inputOrder"],
-													    value=value, label=label, visible=True),
+													    value=chkbox_value, label=chkbox_label, visible=True),
 		                step3_btn : gr.Button(visible=True)}
 	
-	fillmode_btn.click(
-	    fn = fill_value,
-	    inputs = [app_state_json, channel_info_json, in_fill_mode],
-		outputs = [app_state_json, desc_md, in_fill_mode, fillmode_btn, chkbox_group, step3_btn, next_btn, run_btn]
-	).success(
-	    fn = None,
-	    js = init_js,
-	    inputs = [app_state_json, channel_info_json],
-		outputs = []
-	)
-	
 	def update_chkbox(app_state, channel_info, selected):
 	
 		# save info before clicking on next_btn
@@ -674,6 +709,17 @@ with gr.Blocks() as demo:
 			return {app_state_json : app_state,
 					chkbox_group : gr.CheckboxGroup(value=chkbox_value, label=chkbox_label)}
 	
+	fillmode_btn.click(
+	    fn = fill_value,
+	    inputs = [app_state_json, channel_info_json, in_fill_mode],
+		outputs = [app_state_json, desc_md, in_fill_mode, fillmode_btn, chkbox_group, step3_btn, next_btn, run_btn]
+	).success(
+	    fn = None,
+	    js = init_js,
+	    inputs = [app_state_json, channel_info_json],
+		outputs = []
+	)
+	
 	step3_btn.click(
 	    fn = update_chkbox,
 	    inputs = [app_state_json, channel_info_json, chkbox_group],
@@ -686,17 +732,16 @@ with gr.Blocks() as demo:
 		outputs = []
 	)
 	
-    
+    # -------------------------stage2: decode data-------------------------------
 	def delete_file(filename):
 		try:
 			os.remove(filename)
 		except OSError as e:
 			print(e)
 	
-	# stage2
 	def reset_run(app_state, channel_info, raw_data, model_name):
 	    
-	    # reset in.assigned back to the state after Stage1
+	    # reset in.assigned back to the state after stage1
 		for channel in app_state["stage1UnassignedInputs"]:
 			channel_info["inputDict"][channel]["assigned"] = False
 		
@@ -725,7 +770,7 @@ with gr.Blocks() as demo:
 				batch_md : gr.Markdown(visible=False),
 				out_denoised_data : gr.File(visible=False)}
 	
-	def run_model(app_state, channel_info, raw_data, model_name, fill_mode):
+	def run_model(app_state, channel_info, raw_data, model_name):
 		filepath = app_state["filepath"]
 		samplerate = app_state["sampleRate"]
 		new_filename = app_state["filenames"]["denoised"]
@@ -738,7 +783,7 @@ with gr.Blocks() as demo:
 			yield {batch_md : gr.Markdown(md, visible=True)}
 			
 			if app_state["batchCount"] > 1:
-				app_state, channel_info = mapping_stage2(app_state, channel_info, fill_mode)
+				app_state, channel_info = mapping_stage2(app_state, channel_info)
 				if app_state["runningState"] == "finished":
 					#yield {batch_md : gr.Markdown("error", visible=True)}
 					break
@@ -748,7 +793,7 @@ with gr.Blocks() as demo:
 			total_file_num = utils.preprocessing(filepath, 'mapped.csv', samplerate)
 			# step2: Signal reconstruction
 			utils.reconstruct(model_name, total_file_num, filepath, 'denoised.csv', samplerate)
-			reorder_to_origin(app_state, channel_info, filepath+'denoised.csv', new_filename)
+			reorder_to_origin(app_state, channel_info, new_filename)
 			
 			#if model_name == "(mapped data)":
 				#return {out_denoised_data : filepath + 'mapped.csv'}
@@ -770,7 +815,7 @@ with gr.Blocks() as demo:
 		
 	).success(
 		fn = run_model,
-		inputs = [app_state_json, channel_info_json, in_raw_data, in_model_name, in_fill_mode],
+		inputs = [app_state_json, channel_info_json, in_raw_data, in_model_name],
 		outputs = [run_btn, batch_md, out_denoised_data]
 	)
 	

channel_mapping.py

@@ -22,20 +22,21 @@ def reorder_to_template(app_state, filename):
 	old_data = np.concatenate((old_data, zero_arr), axis=0)
 	
 	for i in range(30):
-		curr_idx_set = old_idx[i]
-		#print("channel_{}'s index set: {}".format(i, curr_idx_set))
+		idx_set = old_idx[i]
+		#print("channel_{}'s index set: {}".format(i, idx_set))
 		
-		if curr_idx_set == []:
+		if idx_set == []:
 			new_data[i, :] = zero_arr
 		else:
-			tmp_data = [old_data[j, :] for j in curr_idx_set]
+			tmp_data = [old_data[j, :] for j in idx_set]
 			new_data[i, :] = np.mean(tmp_data, axis=0)
 	
 	print('old.shape, new.shape: ', old_data.shape, new_data.shape)
 	utils.save_data(new_data, new_filename)
 	return
 
-def reorder_to_origin(app_state, channel_info, filename, new_filename):
+def reorder_to_origin(app_state, channel_info, new_filename):
+	filename = app_state["filepath"]+'denoised.csv'
 	old_idx = app_state["stage1NewOrder"] if app_state["runningState"]=="stage1" else app_state["stage2NewOrder"]
 	old_data = utils.read_train_data(filename) # denoised data
 	template_order = channel_info["templateOrder"]
@@ -48,7 +49,7 @@ def reorder_to_origin(app_state, channel_info, filename, new_filename):
 	for i, channel in enumerate(template_order):
 		idx_set = old_idx[i]
 		
-		# ignore if this channel doesn't exist
+		# ignore if this channel was filled with fill_mode ('mean' or 'zero')
 		if len(idx_set)==1 and channel_info["templateDict"][channel]["matched"]==True:
 			new_data[idx_set[0], :] = old_data[i, :]
 	
@@ -96,7 +97,7 @@ def align_coords(channel_info, template_montage, input_montage):
 	input_order = channel_info["inputOrder"]
 	matched = [channel for channel in input_order if input_dict[channel]["matched"]==True]
 	
-	# 2-d (for the indication of missing template channel's position when fill_mode:'mean_manual')
+	# 2-d (for the indication of missing template channel's position when fill_mode:'mean')
 	fig = [template_montage.plot(), input_montage.plot()]
 	fig[0].set_size_inches(5.6, 5.6)
 	fig[1].set_size_inches(5.6, 5.6)
@@ -161,7 +162,7 @@ def align_coords(channel_info, template_montage, input_montage):
 	})
 	return channel_info
 
-def find_neighbors(app_state, channel_info, fill_mode):
+def find_neighbors(app_state, channel_info):
 	new_idx = app_state["stage1NewOrder"] if app_state["runningState"]=="stage1" else app_state["stage2NewOrder"]
 	template_dict = channel_info["templateDict"]
 	input_dict = channel_info["inputDict"]
@@ -170,7 +171,7 @@ def find_neighbors(app_state, channel_info, fill_mode):
 	#z_row_idx = channel_info["dataShape"][0]
 	missing_channels = app_state["missingTemplates"]
 	if missing_channels == []:
-		return app_state # change mothing
+		return app_state # change nothing
 	
 	
 	in_coords = [input_dict[channel]["coord"] for channel in input_order]
@@ -254,7 +255,7 @@ def mapping_stage1(app_state, channel_info, loc_file):
 	print('Mapping (stage1) finished in',second2 - second1,'s.')
 	yield app_state, channel_info, gr.Markdown("", visible=False)
 
-def mapping_stage2(app_state, channel_info, fill_mode):
+def mapping_stage2(app_state, channel_info):
 	second1 = time.time()
 
 	template_dict = channel_info["templateDict"]
@@ -312,7 +313,7 @@ def mapping_stage2(app_state, channel_info, fill_mode):
 	})
 	
 	# fill the missing_channels channels
-	app_state = find_neighbors(app_state, channel_info, fill_mode)
+	app_state = find_neighbors(app_state, channel_info)
 	
 	second2 = time.time()
 	print(f'Mapping (stage2-{app_state["batchCount"]-1}) finished in {second2 - second1}s.')