Sidecar Creation from scratch implemented

BIDSHandler/CreationTool/Application.py

@@ -126,11 +126,11 @@ class Application(tk.Frame):
 
         Tools.clean_frame(self.center_frame)
 
-        self.form_handler = FormHandler(self.center_frame, self.selected_forms)
+        self.form_handler = FormHandler(self.center_frame, self.selected_forms, 'res/Requirements.json')
         self.form_handler.show_forms(0)
         self.confirm_button.config(text='Create', command=self.form_finish, state='disabled')
 
-        self.center_frame.winfo_toplevel().bind('<<EntryStateChanged>>', lambda *_: self.check_mandatory(self.form_handler.form_frame_list[0]))
+        self.center_frame.winfo_toplevel().bind('<<EntryStateChanged>>', lambda *_: self.check_mandatory(self.form_handler.form_frame_list[0], self.confirm_button))
 
     def form_finish(self):
         ''' This method is used to finish the creation of the dataset description of the new BIDS project.
@@ -144,7 +144,7 @@ class Application(tk.Frame):
         self.form_handler.show_forms(0)
         self.confirm_button.config(text='Confirm', command=self.next_step, state='disabled')
 
-        self.form_handler.frame.winfo_toplevel().bind('<<EntryStateChanged>>', lambda *_: self.check_mandatory(self.form_handler.form_frame_list[0]))
+        self.form_handler.frame.winfo_toplevel().bind('<<EntryStateChanged>>', lambda *_: self.check_mandatory(self.form_handler.form_frame_list[0], self.confirm_button))
 
     def next_step(self):
         ''' This method is used to go to the next step of the creation of the new BIDS project.
@@ -168,15 +168,15 @@ class Application(tk.Frame):
             self.actual_step += 1
             self.integrate_sidecar()
 
-    def check_mandatory(self, form):
+    def check_mandatory(self, form, validation_button):
         ''' This method is used to check if the form is valid.
 
             The confirm button is enabled if the form is valid.
         '''
         if form.is_valid_mandatory():
-            self.confirm_button.config(state='normal')
+            validation_button.config(state='normal')
         else:
-            self.confirm_button.config(state='disabled')
+            validation_button.config(state='disabled')
 
     def create_directory(self):
         ''' This method is used to create the directory of the new BIDS project.
@@ -429,6 +429,9 @@ class Application(tk.Frame):
         self.integrate_sidecar_button = tk.Button(self.integrate_sidecar_frame, text='Integrate sidecar', command=self.integrate_sidecar_file)
         self.integrate_sidecar_button.pack()
 
+        self.create_sidecar_button = tk.Button(self.integrate_sidecar_frame, text='Create sidecar', command=self.create_sidecar)
+        self.create_sidecar_button.pack()
+
         self.show_project_button = tk.Button(self.integrate_sidecar_frame, text='Show project state', command=self.actual_project_state)
         self.show_project_button.pack()
 
@@ -447,6 +450,87 @@ class Application(tk.Frame):
         self.integrate_sidecar_button = tk.Button(self.integrate_sidecar_window, text='Select file', command=self.select_sidecar_file)
         self.integrate_sidecar_button.grid(row=1, column=0)
 
+
+
+    def create_sidecar(self):
+        ''' This method is used to create a sidecar of the new BIDS project.
+
+            The user is guided through the process of creating a sidecar of the new BIDS project.
+            He is first prompted to select the type of the sidecar (e.g. channels.tsv, events.tsv, etc.).
+        '''
+        self.integrate_sidecar_window = tk.Toplevel(self.root)
+        self.integrate_sidecar_window.title('Create sidecar')
+
+        self.integrate_sidecar_label = tk.Label(self.integrate_sidecar_window, text='Create sidecar')
+        self.integrate_sidecar_label.grid(row=0, column=0)
+
+        self.sidecar_type_label = tk.Label(self.integrate_sidecar_window, text='Select the type of the sidecar:')
+        self.sidecar_type_label.grid(row=1, column=0)
+
+        self.sidecar_type = tk.StringVar()
+        self.sidecar_type.set('channels.tsv')
+        self.sidecar_type_dropdown = ttk.Combobox(self.integrate_sidecar_window, textvariable=self.sidecar_type)
+        self.sidecar_type_dropdown['values'] = self.extension_to_possible_sidecar['edf'] # To change
+        self.sidecar_type_dropdown.grid(row=1, column=1)
+        self.sidecar_type_dropdown.config(state='readonly')
+
+        self.integrate_sidecar_button = tk.Button(self.integrate_sidecar_window, text='Create file', command=self.create_sidecar_second)
+        self.integrate_sidecar_button.grid(row=2, column=0)
+
+    def select_sidecar_type(self):
+        ''' This method is used to select the type of the sidecar to create.
+
+            The user is guided through the process of selecting the type of the sidecar to create.
+        '''
+        self.integrate_sidecar_window.lift()
+        self.integrate_sidecar_label.config(text='Create sidecar\nType selected: ' + self.sidecar_type.get())
+
+        self.change_sidecar_button = tk.Button(self.integrate_sidecar_window, text='Change type', command=self.create_sidecar)
+
+        self.integrate_sidecar_button.config(text='Create', command=self.create_sidecar_second, state='normal')
+
+    def create_sidecar_second(self):
+        ''' This method is used to finish the creation of the sidecar of the new BIDS project.
+
+            Following the type selected, the user is presented with a form to fill that will be saved as the sidecar.
+            For .json files, the form is a dictionary.
+            For .tsv files, the form is a table.
+        '''
+
+        self.integrate_sidecar_window.destroy()
+        self.integrate_sidecar_window = tk.Toplevel(self.root)
+        self.integrate_sidecar_window.title('Create sidecar')
+
+        self.integrate_sidecar_label = tk.Label(self.integrate_sidecar_window, text='Creating sidecar...')
+        self.integrate_sidecar_label.grid(row=0, column=0)
+
+        self.form_handler = FormHandler(self.integrate_sidecar_window, [self.sidecar_type.get()], 'res/Sidecars.json')
+        self.form_handler.show_forms(0)
+
+        self.integrate_sidecar_button = tk.Button(self.integrate_sidecar_window, text='Confirm', command=self.create_sidecar_finish, state='disabled')
+        self.integrate_sidecar_button.grid(row=1, column=0)
+
+        self.form_handler.frame.winfo_toplevel().bind('<<EntryStateChanged>>', lambda *_: self.check_mandatory(self.form_handler.form_frame_list[0], self.integrate_sidecar_button))
+
+    def create_sidecar_finish(self):
+        ''' This method is used to finish the creation of the sidecar of the new BIDS project.
+
+            The sidecar is temporarily saved in the res folder of the application.
+            The user is then prompted to select the experiments to apply the sidecar to.
+        '''
+        self.sidecar_file = self.project_directory + '/' + 'res/' + self.sidecar_type.get()
+        os.mkdir(self.project_directory + '/' + 'res')
+        self.form_handler.save_forms(0, self.project_directory + '/' + 'res')
+        self.form_handler.form_frame_list[0].frame.grid_forget()
+        self.form_handler.form_frame_list[0].frame.destroy()
+        self.form_handler.form_frame_list.pop(0)
+        self.experiments_files = []
+
+        self.integrate_sidecar_label.config(text='Sidecar created')
+        self.integrate_sidecar_button.config(text='Select experiments', command=lambda: self.select_experiments(True), state='normal')
+
+
+
     def select_sidecar_file(self):
         ''' This method is used to select the file to integrate to the new BIDS project.
 
@@ -466,25 +550,30 @@ class Application(tk.Frame):
         self.sidecar_type_dropdown = ttk.Combobox(self.integrate_sidecar_window, textvariable=self.sidecar_type)
         self.sidecar_type_dropdown['values'] = self.extension_to_possible_sidecar['edf'] # To change
         self.sidecar_type_dropdown.grid(row=2, column=1)
+        self.sidecar_type_dropdown.config(state='readonly')
 
         self.integrate_sidecar_button.config(text='Select experiments', command=self.select_experiments)
         self.experiments_files = []
 
-    def select_experiments(self):
+    def select_experiments(self, create=False):
         ''' This method is used to select the experiments to apply the sidecar to.
 
             The user is guided through the process of selecting the experiments to apply the sidecar to.
         '''
+        if not create:
             self.sidecar_type_dropdown.grid_forget()
             self.dropdown_label.grid_forget()
         self.experiments_files.append(tk.filedialog.askopenfilename(initialdir=self.project_directory))
         self.integrate_sidecar_window.lift()
         self.integrate_sidecar_label.config(text='File selected: ' + self.sidecar_file + '\nType: ' + self.sidecar_type.get() + '\nExperiments selected: ' + str(self.experiments_files))
 
-        self.add_experiment_button = tk.Button(self.integrate_sidecar_window, text='Add experiment', command=self.select_experiments)
+        self.add_experiment_button = tk.Button(self.integrate_sidecar_window, text='Add experiment', command= lambda : self.select_experiments(create))
         self.add_experiment_button.grid(row=2, column=0)
 
+        if not create:
             self.integrate_sidecar_button.config(text='Integrate', command=self.integrate_sidecar_finish, state='normal')
+        else:
+            self.integrate_sidecar_button.config(text='Integrate', command=self.place_created_sidecar, state='normal')
 
     def integrate_sidecar_finish(self):
         ''' This method is used to finish the integration of the sidecar to the new BIDS project.
@@ -611,3 +700,30 @@ class Application(tk.Frame):
             if value != 'not_shared':
                 res = res + key + '-' + value + '_'
         return res
+
+    def place_created_sidecar(self):
+        ''' This method is used to place the created sidecar to the new BIDS project.
+
+            The created sidecar is placed to the new BIDS project.
+            It is saved following the bids standard on inheritance.
+            It is placed at the optimal place in the hierarchy to be applied to the choosen experiments.
+            It is named following the BIDS standard.
+        '''
+        self.integrate_sidecar_window.destroy()
+        self.integrate_sidecar_window = tk.Toplevel(self.root)
+        self.integrate_sidecar_window.title('Integrate sidecar')
+
+        self.integrate_sidecar_label = tk.Label(self.integrate_sidecar_window, text='Placing sidecar...')
+        self.integrate_sidecar_label.grid(row=0, column=0)
+
+        self.integrate_sidecar_button = tk.Button(self.integrate_sidecar_window, text='Leave', command=self.integrate_sidecar_window.destroy)
+        self.integrate_sidecar_button.grid(row=1, column=0)
+
+        path = self.get_optimal_files(self.experiments_files, self.sidecar_type.get())
+
+        for p in path:
+            shutil.copy2(self.sidecar_file, p)
+
+        shutil.rmtree(self.project_directory + '/' + 'res')
+        self.integrate_sidecar_label.config(text='Sidecar placed')
+

BIDSHandler/CreationTool/FormHandler.py

@@ -146,10 +146,10 @@ class Form:
 
 class FormHandler:
 
-    def __init__(self, frame, necessary_forms):
+    def __init__(self, frame, necessary_forms, file_path):
         self.frame = frame
         self.form_frame_list = []
-        self.requirement = json.load(open(os.path.join(os.path.dirname(__file__), 'res/Requirements.json')))
+        self.file = json.load(open(os.path.join(os.path.dirname(__file__), file_path)))
 
         with Image.open(os.path.join(os.path.dirname(__file__), 'res/help_icon.png')) as img_help:
             img_help = img_help.resize((20, 20))
@@ -161,7 +161,7 @@ class FormHandler:
             img_valid = img_valid.resize((20, 20))
             self.valid_icon = ImageTk.PhotoImage(img_valid)
 
-        for form in self.requirement.items():
+        for form in self.file.items():
             if form[0] in necessary_forms:
                 self.form_frame_list.append(Form(form, self.frame, self.help_icon, self.invalid_icon, self.valid_icon))
 

BIDSHandler/CreationTool/res/Sidecars.json

+{
+  "channels.tsv" : {
+    "name": {
+      "requirement level": "required",
+      "description": "Label of the channel, values must be unique",
+      "valid condition": "len(value) > 0"
+    },
+    "type": {
+      "requirement level": "required",
+      "description": "Type of the channel",
+      "valid condition": "len(value) > 0"
+    },
+    "units": {
+      "requirement level": "required",
+      "description": "Physical unit of the value represented in this channel, for example, V for Volt, or fT/cm for femto Tesla per centimeter",
+      "valid condition": "len(value) > 0"
+    },
+    "description": {
+      "requirement level": "optional",
+      "description": "Brief free-text description of the channel, or other information of interest.",
+      "valid condition": "len(value) > 0"
+    },
+    "sampling_frequency": {
+      "requirement level": "required",
+      "description": "Sampling frequency of the channel in Hz",
+      "valid condition": "float(value) > 0"
+    },
+    "reference": {
+      "requirement level": "optional",
+      "description": "Name of the reference electrode(s). This column is not needed when it is common to all channels. In that case the reference electrode(s) can be specified in *_eeg.json as EEGReference).",
+      "valid condition": "len(value) > 0"
+    },
+    "low_cutoff": {
+      "requirement level": "optional",
+      "description": "Frequencies used for the high-pass filter applied to the channel in Hz. If no high-pass filter applied, use n/a.",
+      "valid condition": "value == 'n/a' or float(value) > 0"
+    },
+    "high_cutoff": {
+      "requirement level": "optional",
+      "description": "Frequencies used for the low-pass filter applied to the channel in Hz. If no low-pass filter applied, use n/a. Note that hardware anti-aliasing in A/D conversion of all MEG/EEG electronics applies a low-pass filter; specify its frequency here if applicable.",
+      "valid condition": "value == 'n/a' or float(value) > 0"
+    },
+    "notch": {
+      "requirement level": "optional",
+      "description": "Frequencies used for the notch filter applied to the channel, in Hz. If notch filters are applied at multiple frequencies, these frequencies MAY be specified as a list, for example, [60, 120, 180]. If no notch filter was applied, use n/a.",
+      "valid condition": "value == 'n/a' or float(value) > 0",
+      "multiple": true
+    },
+    "status": {
+      "requirement level": "optional",
+      "description": "Frequencies used for the notch filter applied to the channel, in Hz. If notch filters are applied at multiple frequencies, these frequencies MAY be specified as a list, for example, [60, 120, 180]. If no notch filter was applied, use n/a.",
+      "valid condition": "value in ['good', 'bad', 'n/a']",
+      "multiple": false
+    },
+    "status_description": {
+      "requirement level": "optional",
+      "description": "Freeform text description of noise or artifact affecting data quality on the channel. It is meant to explain why the channel was declared bad in the status column.",
+      "valid condition": "len(value) > 0",
+      "multiple": false
+    }
+  }
+
+
+}
\ No newline at end of file