jupyter notebook widget for qc

mooda/__init__.py

@@ -1,6 +1,7 @@
 """ Implementation of mooda """
 from .waterframe import WaterFrame
 from .input import read_nc_emodnet, read_nc, read_nc_imos, read_pkl, read_nc_moist
-from .util import concat, iplot_location, iplot_timeseries, md5, es_create_indexes
+from .util import concat, iplot_location, iplot_timeseries, md5, \
+    es_create_indexes, Widgets
 
 __version__ = '1.7.0'

mooda/util/__init__.py

@@ -3,4 +3,5 @@
 from .iplot import iplot_location, iplot_timeseries
 from .md5 import md5
 from .es_create_indexes import es_create_indexes
-from .emso import EMSO
+from .emso import EMSO
+from .md_widgets import Widgets

mooda/util/md_widgets.py

@@ -0,0 +1,160 @@
+import ipywidgets as widgets
+from IPython.display import clear_output
+from typing import List, List
+from ..input import read_pkl
+import plotly.offline as pyo
+
+pyo.init_notebook_mode()
+
+class Widgets:
+
+    @staticmethod
+    def qc(filename, parameter: str,
+           range_test: List[float]=[-1000, 1000], spike_window: int=100,
+           spike_threshold: float=3.5, spike_influence: float=0.5):
+        """
+        It makes a QC Jupyter Widget
+
+        Parameters
+        ----------
+            filename: str
+                Location of the pickle file with the dataset
+            parameter: str
+                Parameter
+            range_test: List[float]
+                Limits for the range test [min value, max value]
+
+        Returns
+        -------
+            main_box: ipwidgets.VBox
+                Jupyter notebook widget 
+        """
+
+        def show_result(wf, parameter_in, chart_title=''):
+            # Change name of flags
+            wf2 = wf.copy()
+            qc_labels = {0: 'No QC', 1: 'Good data', 4: 'Bad data'}
+            wf2.data[f'{parameter}_QC'].replace(qc_labels, inplace=True)
+
+            fig = wf2.iplot_line(
+                parameter,
+                color='TEMP_QC',
+                marginal_y=None,
+                line_shape='linear',
+                rangeslider_visible=False,
+                line_dash_sequence=['dot', 'dot'],
+                title=chart_title)
+            fig.show()
+
+        # Flat test
+        flat_label = widgets.Label('Flat test:')
+        window_flat = widgets.IntText(value=2,
+                                      description='Window:',
+                                      disabled=False,
+                                      color='black')
+        flat_checkbox = widgets.Checkbox(description='Do it!')
+
+        # Range test
+        range_label = widgets.Label('Range test:')
+        range_checkbox = widgets.Checkbox(description='Do it!')
+        limits = widgets.FloatRangeSlider(value=[range_test[0], range_test[1]],
+                                          min=range_test[0],
+                                          max=range_test[1],
+                                          step=0.1,
+                                          description='Limits:',
+                                          disabled=False,
+                                          continuous_update=False,
+                                          orientation='horizontal',
+                                          readout=True,
+                                          readout_format='.1f')
+
+        # Spike test
+        spike_label = widgets.Label('Spike test:')
+        spike_checkbox = widgets.Checkbox(description='Do it!')
+        window_spike = widgets.IntText(value=spike_window,
+                                       description='Window:', disabled=False,
+                                       color='black')
+        threshold = widgets.FloatText(value=spike_threshold,
+                                      description='Threshold:', disabled=False,
+                                      color='black')
+        influence = widgets.FloatSlider(
+            value=spike_influence,
+            min=0,
+            max=1,
+            step=0.1,
+            description='Influence:',
+            disabled=False,
+            continuous_update=False,
+            orientation='horizontal',
+            readout=True,
+            readout_format='.1f',
+            slider_color='white'
+        )
+
+        # Replace
+        replace_label = widgets.Label('Replace QC:')
+        replace_checkbox = widgets.Checkbox(description='Do it!')
+
+        # Button
+        button = widgets.Button(description='Run tests')
+        out = widgets.Output()
+        def on_button_clicked(_):
+            # "linking function with output"
+            with out:
+                # what happens when we press the button
+                clear_output()
+                wf = read_pkl(filename)
+
+                if parameter in wf.parameters:
+                    print(wf)
+                    print()
+                    show_result(wf, parameter, 
+                                'Values without apply any QC test')
+                    print()
+
+                    if flat_checkbox.value:
+                        print(window_flat.value)
+                        wf.qc_flat_test(window=window_flat.value)
+                        show_result(wf, parameter, 
+                                    'Values after apply the flat test. ' + \
+                                    ' Configuration flat test: window = ' + \
+                                    f'{window_flat.value}')
+                        print()
+                    if range_checkbox.value:
+                        wf.qc_range_test(limits=limits.value)
+                        show_result(wf, parameter,
+                                    'Values after apply the flat test and ' + \
+                                        'the range test. Configuration ' + \
+                                        f'range test: limits = {limits.value}')
+                        print()
+                    if spike_checkbox.value:
+                        wf.qc_spike_test(window=window_spike.value,
+                                         influence=influence.value,
+                                         threshold=threshold.value)
+                        show_result(wf, parameter,
+                                    'Values after apply the flat test, the ' \
+                                        'range test and the spike test.' + \
+                                        ' Configuration spike test: window ' \
+                                        f'= {window_spike.value}, ' \
+                                        f'influence = {influence.value}, ' + \
+                                        f'threshold = {threshold.value}')
+                        print()
+                    if replace_checkbox.value:
+                        wf.qc_replace()
+                        show_result(wf, parameter, f'Final result')
+                else:
+                    print(f'Parameter {parameter} not in {wf.parameters}')
+
+        # linking button and function together using a button's method
+        button.on_click(on_button_clicked)
+
+        flat_box = widgets.HBox([flat_label, flat_checkbox, window_flat])
+        range_box = widgets.HBox([range_label, range_checkbox, limits])
+        spike_column = widgets.VBox([window_spike, threshold, influence])
+        spike_box = widgets.HBox([spike_label, spike_checkbox, spike_column])
+        replace_box = widgets.HBox([replace_label, replace_checkbox])
+
+        main_box = widgets.VBox([flat_box, range_box, spike_box, replace_box,
+                                 button, out])
+
+        return main_box