ENH: Added feature to load single .csv files from the gui

STY: Fixed edge case on dropdown width. Fixed flake8 errors MAINT: Moving save simulation button initialization logic to a private funciton. Adding upload csv file test DOC: Added entry in whats_new.rst DOC: Update doc/whats_new.rst Co-authored-by: George Dang <[email protected]> TEST: Fixed csv file upload test on windows MAINT: Removed commented code STY: Fixed docustring of the public funciton serialize_simulation STY: Applied changes in docustirng of serialize_simulation TST: Added new test cases on test_gui_upload_csv_simulation. Fixed flake8 errors
brown-ccv · May 8, 2024 · b78b8ba · b78b8ba
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diff --git a/doc/whats_new.rst b/doc/whats_new.rst
@@ -55,6 +55,9 @@ Changelog
 - Added gui widget to enable/disable synchronous input in simulations, 
   by `Camilo Diaz`_ in :gh:`750`
 
+- Added gui widgets to save simulation as csv and updated the file upload to support csv data,
+  by `Camilo Diaz`_ in :gh:`753`
+
 Bug
 ~~~
 - Fix inconsistent connection mapping from drive gids to cell gids, by

diff --git a/hnn_core/__init__.py b/hnn_core/__init__.py
@@ -1,4 +1,4 @@
-from .dipole import simulate_dipole, read_dipole, average_dipoles, Dipole
+from .dipole import simulate_dipole, read_dipole, average_dipoles, Dipole,_read_dipole_txt
 from .params import Params, read_params, convert_to_hdf5
 from .network import Network, pick_connection
 from .network_models import jones_2009_model, law_2021_model, calcium_model

diff --git a/hnn_core/dipole.py b/hnn_core/dipole.py
@@ -106,20 +106,25 @@ def simulate_dipole(net, tstop, dt=0.025, n_trials=None, record_vsec=False,
     return dpls
 
 
-def _read_dipole_txt(fname):
+def _read_dipole_txt(fname, extension='.txt'):
     """Read dipole values from a txt file and create a Dipole instance.
 
     Parameters
     ----------
-    fname : str
-        Full path to the input file (.txt)
-
+    fname : str or io.StringIO
+        Full path to the input file (.txt or .csv) or
+        Content of file in memory as a StringIO
     Returns
     -------
     dpl : Dipole
         The instance of Dipole class
     """
-    dpl_data = np.loadtxt(fname, dtype=float)
+    if extension == '.csv':
+        # read from a csv file ignoring the headers
+        dpl_data = np.genfromtxt(fname, delimiter=',',
+                                 skip_header=1, dtype=float)
+    else:
+        dpl_data = np.loadtxt(fname, dtype=float)
     ncols = dpl_data.shape[1]
     if ncols not in (2, 4):
         raise ValueError(
@@ -174,10 +179,6 @@ def read_dipole(fname):
         The instance of Dipole class
     """
 
-    # For supporting tests in test_gui.py
-    if isinstance(fname, StringIO):
-        return _read_dipole_txt(fname)
-
     fname = str(fname)
     if not os.path.exists(fname):
         raise FileNotFoundError('File not found at path %s.' % (fname,))

diff --git a/hnn_core/gui/gui.py b/hnn_core/gui/gui.py
@@ -234,35 +234,18 @@ def __init__(self, theme_color="#8A2BE2",
                                             description='Cores:',
                                             disabled=False)
         self.load_data_button = FileUpload(
-            accept='.txt', multiple=False,
+            accept='.txt,.csv', multiple=False,
             style={'button_color': self.layout['theme_color']},
             description='Load data',
             button_style='success')
 
-        b64 = base64.b64encode("".encode())
-        payload = b64.decode()
-        # Initialliting HTML code for download button
-        self.html_download_button = '''
-        <a download="{filename}" href="data:text/csv;base64,{payload}"
-          download>
-        <button style="background:{color_theme}; height:{btn_height}"
-        class=" jupyter-button
-           mod-warning" {is_disabled} >Save Simulation</button>
-        </a>
-        '''
-        # Create widget wrapper
-        self.save_simuation_button = (
-            HTML(self.html_download_button.
-                 format(payload=payload,
-                        filename={""},
-                        is_disabled="disabled",
-                        btn_height=self.layout['run_btn'].height,
-                        color_theme=self.layout['theme_color'])))
+        # Create save simulation widget wrapper
+        self.save_simuation_button = self._init_html_download_button()
 
         self.simulation_list_widget = Dropdown(options=[],
                                                value=None,
                                                description='',
-                                               layout={'width': 'max-content'})
+                                               layout={'width': '15%'})
         # Drive selection
         self.widget_drive_type_selection = RadioButtons(
             options=['Evoked', 'Poisson', 'Rhythmic'],
@@ -315,6 +298,27 @@ def __init__(self, theme_color="#8A2BE2",
         self._init_ui_components()
         self.add_logging_window_logger()
 
+    def _init_html_download_button(self):
+        b64 = base64.b64encode("".encode())
+        payload = b64.decode()
+        # Initialliting HTML code for download button
+        self.html_download_button = '''
+        <a download="{filename}" href="data:text/csv;base64,{payload}"
+          download>
+        <button style="background:{color_theme}; height:{btn_height}"
+        class=" jupyter-button
+           mod-warning" {is_disabled} >Save Simulation</button>
+        </a>
+        '''
+        # Create widget wrapper
+        return (
+            HTML(self.html_download_button.
+                 format(payload=payload,
+                        filename={""},
+                        is_disabled="disabled",
+                        btn_height=self.layout['run_btn'].height,
+                        color_theme=self.layout['theme_color'])))
+
     def add_logging_window_logger(self):
         handler = _OutputWidgetHandler(self._log_out)
         handler.setFormatter(
@@ -1211,7 +1215,10 @@ def on_upload_data_change(change, data, viz_manager, log_out):
 
     data_dict = change['new'][0]
 
-    data_fname = data_dict['name'].rstrip('.txt')
+    dict_name = data_dict['name'].rsplit('.', 1)
+    data_fname = dict_name[0]
+    file_extension = f".{dict_name[1]}"
+
     if data_fname in data['simulation_data'].keys():
         logger.error(f"Found existing data: {data_fname}.")
         return
@@ -1220,7 +1227,7 @@ def on_upload_data_change(change, data, viz_manager, log_out):
     ext_content = codecs.decode(ext_content, encoding="utf-8")
     with log_out:
         data['simulation_data'][data_fname] = {'net': None, 'dpls': [
-            hnn_core.read_dipole(io.StringIO(ext_content))
+            hnn_core._read_dipole_txt(io.StringIO(ext_content), file_extension)
         ]}
         logger.info(f'External data {data_fname} loaded.')
         _template_name = "[Blank] single figure"
@@ -1444,23 +1451,11 @@ def _serialize_simulation(log_out, sim_data, simulation_list_widget):
 
 
 def serialize_simulation(simulations_data, simulation_name):
-    """
-        Serializes the simulation data for a given simulation name
-        into either a single CSV file
-        or a ZIP file containing multiple CSVs, depending on the number
-        of trials in the simulation.
-        Parameters:
-        - simulation_name (str): The name of the simulation to serialize.
-                                 This name is used to access the corresponding
-                                 data in the 'simulations' dictionary
-                                 of the instance.
-
-        Returns:
-        - tuple: A tuple where the first element is either
-                the CSV content (str) of a single trial
-                or the binary data of a ZIP file (bytes)
-                containing multiple CSV files, and the
-                second element is the file extension (either ".csv" or ".zip").
+    """Serializes simulation data to CSV.
+
+        Creates a single CSV file or a ZIP file containing multiple CSVs,
+        depending on the number of trials in the simulation.
+
     """
     simulation_data = simulations_data["simulation_data"]
     csv_trials_output = []

diff --git a/hnn_core/tests/assets/test_default.csv b/hnn_core/tests/assets/test_default.csv
@@ -0,0 +1,202 @@
+# times,agg,L2,L5
+0.000000, 0.004901, -0.000004, 0.004905
+0.850000, -0.001031, -0.000002, -0.001028
+1.700000, -0.000821, -0.000001, -0.000820
+2.550000, -0.000643, -0.000000, -0.000642
+3.400000, -0.000500, -0.000000, -0.000500
+4.250000, -0.000389, 0.000000, -0.000389
+5.100000, -0.000304, 0.000000, -0.000305
+5.950000, -0.000240, 0.000000, -0.000240
+6.800000, -0.000190, 0.000000, -0.000191
+7.650000, -0.000153, 0.000000, -0.000153
+8.500000, -0.000125, 0.000000, -0.000125
+9.350000, -0.000105, 0.000000, -0.000105
+10.200000, -0.000091, 0.000000, -0.000091
+11.050000, -0.000081, 0.000000, -0.000082
+11.900000, -0.000076, 0.000000, -0.000077
+12.750000, -0.000074, 0.000000, -0.000075
+13.600000, -0.000075, 0.000000, -0.000076
+14.450000, -0.000078, 0.000000, -0.000078
+15.300000, -0.000083, 0.000000, -0.000083
+16.150000, -0.000089, 0.000000, -0.000089
+17.000000, -0.000095, 0.000000, -0.000096
+17.850000, -0.000103, 0.000000, -0.000103
+18.700000, -0.000111, 0.000000, -0.000111
+19.550000, -0.000119, 0.000000, -0.000119
+20.400000, -0.000036, 0.000091, -0.000127
+21.250000, 0.000111, 0.000246, -0.000135
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+22.950000, 0.000023, 0.000100, -0.000076
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+24.650000, 0.001068, 0.000864, 0.000204
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+28.900000, 0.010487, 0.005213, 0.005274
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+30.600000, 0.011241, 0.006422, 0.004819
+31.450000, 0.009575, 0.006133, 0.003442
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+33.150000, 0.006574, 0.003111, 0.003463
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+97.750000, -0.009078, -0.001202, -0.007876
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