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 <53052793+gtdang@users.noreply.github.com> 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 · 5e04b17 · 5e04b17
1 parent abd6ee4
commit 5e04b17
Show file tree

Hide file tree

Showing 6 changed files with 289 additions and 50 deletions.
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
+22.100000, 0.000440, 0.000583, -0.000143
+22.950000, 0.000023, 0.000100, -0.000076
+23.800000, 0.000069, -0.000005, 0.000074
+24.650000, 0.001068, 0.000864, 0.000204
+25.500000, 0.002378, 0.002052, 0.000326
+26.350000, 0.003182, 0.002578, 0.000604
+27.200000, 0.003840, 0.002685, 0.001155
+28.050000, 0.007157, 0.003880, 0.003277
+28.900000, 0.010487, 0.005213, 0.005274
+29.750000, 0.011173, 0.006169, 0.005004
+30.600000, 0.011241, 0.006422, 0.004819
+31.450000, 0.009575, 0.006133, 0.003442
+32.300000, 0.009335, 0.005203, 0.004132
+33.150000, 0.006574, 0.003111, 0.003463
+34.000000, 0.002448, 0.000363, 0.002086
+34.850000, -0.000186, -0.001311, 0.001125
+35.700000, -0.003248, -0.000321, -0.002928
+36.550000, -0.005199, 0.001513, -0.006712
+37.400000, -0.005465, 0.002522, -0.007986
+38.250000, -0.004499, 0.003356, -0.007855
+39.100000, -0.003944, 0.002935, -0.006879
+39.950000, -0.003525, 0.001841, -0.005365
+40.800000, -0.003617, 0.000354, -0.003971
+41.650000, -0.003927, -0.000611, -0.003316
+42.500000, -0.004465, -0.001302, -0.003162
+43.350000, -0.004995, -0.001412, -0.003584
+44.200000, -0.005744, -0.000842, -0.004902
+45.050000, -0.007144, -0.000433, -0.006711
+45.900000, -0.008093, -0.000461, -0.007633
+46.750000, -0.008008, 0.000093, -0.008101
+47.600000, -0.007503, 0.000971, -0.008474
+48.450000, -0.005630, 0.001635, -0.007265
+49.300000, -0.003517, 0.001869, -0.005386
+50.150000, -0.002863, 0.001902, -0.004765
+51.000000, -0.005328, 0.001636, -0.006964
+51.850000, -0.007813, 0.001029, -0.008842
+52.700000, -0.005764, 0.000967, -0.006731
+53.550000, -0.001065, 0.001102, -0.002166
+54.400000, 0.000317, 0.001231, -0.000914
+55.250000, 0.001767, 0.001268, 0.000500
+56.100000, 0.004760, 0.001304, 0.003456
+56.950000, 0.005124, 0.001289, 0.003835
+57.800000, 0.002286, 0.001216, 0.001070
+58.650000, -0.000461, 0.001093, -0.001554
+59.500000, -0.002546, 0.000963, -0.003508
+60.350000, -0.004627, 0.000811, -0.005438
+61.200000, -0.006834, 0.000671, -0.007505
+62.050000, -0.008932, 0.000516, -0.009449
+62.900000, -0.013852, 0.000352, -0.014203
+63.750000, -0.018401, 0.000157, -0.018559
+64.600000, -0.024898, -0.000071, -0.024827
+65.450000, -0.032659, -0.000282, -0.032377
+66.300000, -0.039890, -0.000617, -0.039273
+67.150000, -0.048405, -0.000906, -0.047499
+68.000000, -0.057989, -0.001351, -0.056637
+68.850000, -0.059963, -0.001943, -0.058020
+69.700000, -0.048681, -0.002180, -0.046500
+70.550000, -0.031704, -0.002144, -0.029560
+71.400000, -0.017230, -0.002095, -0.015135
+72.250000, -0.020491, -0.002083, -0.018408
+73.100000, -0.010235, -0.001987, -0.008248
+73.950000, -0.000233, -0.001868, 0.001635
+74.800000, 0.006187, -0.001794, 0.007981
+75.650000, 0.004787, -0.001772, 0.006559
+76.500000, -0.000787, -0.001764, 0.000977
+77.350000, -0.003187, -0.001749, -0.001437
+78.200000, 0.006586, -0.001727, 0.008312
+79.050000, 0.004913, -0.001699, 0.006612
+79.900000, 0.002309, -0.001669, 0.003978
+80.750000, -0.003490, -0.001637, -0.001853
+81.600000, -0.002349, -0.001604, -0.000745
+82.450000, 0.007867, -0.001597, 0.009465
+83.300000, 0.013894, -0.001576, 0.015470
+84.150000, 0.009662, -0.001546, 0.011208
+85.000000, -0.004782, -0.001515, -0.003267
+85.850000, -0.015327, -0.001483, -0.013844
+86.700000, -0.019231, -0.001493, -0.017738
+87.550000, -0.023699, -0.001479, -0.022220
+88.400000, -0.027380, -0.001454, -0.025926
+89.250000, -0.029593, -0.001427, -0.028167
+90.100000, -0.030457, -0.001399, -0.029058
+90.950000, -0.027972, -0.001373, -0.026599
+91.800000, -0.023526, -0.001347, -0.022180
+92.650000, -0.027878, -0.001320, -0.026558
+93.500000, -0.034506, -0.001295, -0.033210
+94.350000, -0.037153, -0.001273, -0.035881
+95.200000, -0.034914, -0.001253, -0.033661
+96.050000, -0.028039, -0.001235, -0.026804
+96.900000, -0.020244, -0.001218, -0.019026
+97.750000, -0.009078, -0.001202, -0.007876
+98.600000, -0.002269, -0.001186, -0.001083
+99.450000, 0.002204, -0.001170, 0.003374
+100.300000, 0.005398, -0.001155, 0.006553
+101.150000, 0.005492, -0.001140, 0.006632
+102.000000, 0.003259, -0.001125, 0.004384
+102.850000, 0.015135, -0.001110, 0.016245
+103.700000, 0.017619, -0.001096, 0.018715
+104.550000, 0.018101, -0.001082, 0.019183
+105.400000, 0.018124, -0.001155, 0.019280
+106.250000, 0.020798, -0.001170, 0.021968
+107.100000, 0.023153, -0.001178, 0.024331
+107.950000, 0.022969, -0.001165, 0.024134
+108.800000, 0.020145, -0.001160, 0.021305
+109.650000, 0.018732, -0.001146, 0.019877
+110.500000, 0.016862, -0.001128, 0.017990
+111.350000, 0.011694, -0.000813, 0.012507
+112.200000, 0.007697, -0.000498, 0.008195
+113.050000, 0.003436, -0.000598, 0.004034
+113.900000, 0.001065, -0.001218, 0.002283
+114.750000, 0.001018, -0.001386, 0.002405
+115.600000, 0.001123, -0.001332, 0.002455
+116.450000, 0.000912, -0.001187, 0.002099
+117.300000, 0.001343, -0.000987, 0.002330
+118.150000, 0.003930, -0.000771, 0.004701
+119.000000, 0.007365, -0.000556, 0.007921
+119.850000, 0.008765, -0.000453, 0.009217
+120.700000, 0.010135, -0.000404, 0.010539
+121.550000, 0.012114, -0.000089, 0.012203
+122.400000, 0.014030, 0.000210, 0.013820
+123.250000, 0.012956, 0.000012, 0.012944
+124.100000, 0.009596, -0.000030, 0.009625
+124.950000, 0.009737, 0.001321, 0.008416
+125.800000, 0.011428, 0.002215, 0.009213
+126.650000, 0.009874, 0.001135, 0.008738
+127.500000, 0.007932, 0.000147, 0.007785
+128.350000, 0.008005, 0.000672, 0.007333
+129.200000, 0.008103, 0.000770, 0.007334
+130.050000, 0.007523, -0.000085, 0.007608
+130.900000, 0.011667, 0.001946, 0.009721
+131.750000, 0.016976, 0.004917, 0.012059
+132.600000, 0.018978, 0.004972, 0.014007
+133.450000, 0.018376, 0.003383, 0.014993
+134.300000, 0.018065, 0.004381, 0.013683
+135.150000, 0.018451, 0.005940, 0.012511
+136.000000, 0.017998, 0.006308, 0.011690
+136.850000, 0.016924, 0.005754, 0.011170
+137.700000, 0.022504, 0.008672, 0.013832
+138.550000, 0.025043, 0.011590, 0.013453
+139.400000, 0.029372, 0.011424, 0.017948
+140.250000, 0.032035, 0.009205, 0.022830
+141.100000, 0.034229, 0.009407, 0.024822
+141.950000, 0.033103, 0.011782, 0.021321
+142.800000, 0.030434, 0.012227, 0.018208
+143.650000, 0.027193, 0.009627, 0.017566
+144.500000, 0.018579, 0.006458, 0.012121
+145.350000, 0.006030, 0.001837, 0.004193
+146.200000, 0.000821, -0.000384, 0.001204
+147.050000, 0.003639, 0.001047, 0.002592
+147.900000, 0.010721, 0.004641, 0.006080
+148.750000, 0.020417, 0.009757, 0.010660
+149.600000, 0.024747, 0.013637, 0.011110
+150.450000, 0.026965, 0.014998, 0.011967
+151.300000, 0.030735, 0.014423, 0.016312
+152.150000, 0.035009, 0.014149, 0.020860
+153.000000, 0.036671, 0.011801, 0.024870
+153.850000, 0.035689, 0.009358, 0.026331
+154.700000, 0.031327, 0.008404, 0.022923
+155.550000, 0.026491, 0.008488, 0.018003
+156.400000, 0.024704, 0.007879, 0.016825
+157.250000, 0.023513, 0.006935, 0.016578
+158.100000, 0.021296, 0.005790, 0.015506
+158.950000, 0.022641, 0.005599, 0.017042
+159.800000, 0.022466, 0.006542, 0.015924
+160.650000, 0.018331, 0.007326, 0.011005
+161.500000, 0.014261, 0.007754, 0.006507
+162.350000, 0.013925, 0.007803, 0.006122
+163.200000, 0.013594, 0.007289, 0.006305
+164.050000, 0.010272, 0.006451, 0.003822
+164.900000, 0.007026, 0.005557, 0.001468
+165.750000, 0.002971, 0.005171, -0.002201
+166.600000, 0.002061, 0.005246, -0.003184
+167.450000, 0.003700, 0.005597, -0.001897
+168.300000, 0.007350, 0.005701, 0.001649
+169.150000, 0.010697, 0.005525, 0.005172
+170.000000, 0.013794, 0.005309, 0.008485