Generate plots

cli_util/cli.py

@@ -11,7 +11,11 @@
 import pandas as pd
 import shutil
 import tempfile
-
+import numpy as np
+import matplotlib.pyplot as plt
+import seaborn as sns
+import libsedml as lsed
+from libsedml import SedReport, SedPlot2D
 
 def exec_sed_doc(omex_file_path, base_out_path):
     archive_tmp_dir = tempfile.mkdtemp()
@@ -73,8 +77,99 @@ def transpose_vcml_csv(csv_file_path: str):
     df[final_cols].transpose().to_csv(csv_file_path, header=False, index=False)
 
 
+def get_all_dataref_and_curves(sedml_path):
+    all_plot_curves = {}
+    all_report_dataref = {}
+
+    sedml = lsed.readSedML(sedml_path)
+
+    for output in sedml.getListOfOutputs():
+        if type(output) == SedPlot2D:
+            all_curves = {}
+            for curve in output.getListOfCurves():
+                all_curves[curve.getId()] = {
+                    'x': curve.getXDataReference(),
+                    'y': curve.getYDataReference()
+                }
+            all_plot_curves[output.getId()] = all_curves
+        if type(output) == SedReport:
+            for dataset in output.getListOfDataSets():
+
+                ######
+                if output.getId() in all_report_dataref:
+
+                    all_report_dataref[output.getId()].append({
+                        'data_reference': dataset.getDataReference(),
+                        'data_label': dataset.getLabel()
+                    })
+                else:
+                    all_report_dataref[output.getId()] = []
+                    all_report_dataref[output.getId()].append({
+                        'data_reference': dataset.getDataReference(),
+                        'data_label': dataset.getLabel()
+                    })
+
+
+    return all_report_dataref, all_plot_curves
+
+
+
+def get_report_label_from_data_ref(dataref: str, all_report_dataref):
+    for report in all_report_dataref.keys():
+        for data_ref in all_report_dataref[report]:
+            if dataref == data_ref['data_reference']:
+                return report, data_ref['data_label']
+
+
+### Update plots dict
+
+def update_dataref_with_report_label(all_report_dataref, all_plot_curves):
+
+    for plot,curves in all_plot_curves.items():
+        for curve_name,datarefs in curves.items():
+            new_ref = dict(datarefs)
+            new_ref['x'] = get_report_label_from_data_ref(datarefs['x'], all_report_dataref)[1]
+            new_ref['y'] = get_report_label_from_data_ref(datarefs['y'], all_report_dataref)[1]
+            new_ref['report'] = get_report_label_from_data_ref(datarefs['y'], all_report_dataref)[0]
+            curves[curve_name] = new_ref
+
+    return all_report_dataref, all_plot_curves
+
+
+
+def get_report_dataframes(all_report_dataref, result_out_dir):
+    report_frames = {}
+    reports_list = list(set(all_report_dataref.keys()))
+    for report in reports_list:
+        report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()
+        report_frames[report].columns = report_frames[report].iloc[0].values
+        report_frames[report].drop(index = 0, inplace=True)
+    return report_frames
+
+## PLOTTING
+
+def plot_and_save_curves(all_plot_curves, report_frames, result_out_dir):
+    all_plots = dict(all_plot_curves)
+    for plot, curve_dat in all_plots.items():
+        dims = (12, 8)
+        fig, ax = plt.subplots(figsize=dims)
+        for curve, data in curve_dat.items():
+            df = report_frames[data['report']]
+            sns.lineplot(x=df[data['x']].astype(np.float), y=df[data['y']].astype(np.float), ax=ax, label=curve)
+            ax.set_ylabel('')
+        #         plt.show()
+        plt.savefig(os.path.join(result_out_dir, plot + '.pdf'), dpi=300)
+
+def gen_plot_pdfs(sedml_path, result_out_dir):
+    all_report_dataref, all_plot_curves = get_all_dataref_and_curves(sedml_path)
+    all_report_dataref, all_plot_curves =  update_dataref_with_report_label(all_report_dataref, all_plot_curves)
+    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)
+    plot_and_save_curves(all_plot_curves, report_frames, result_out_dir)
+
+
 if __name__ == "__main__":
     fire.Fire({
         'execSedDoc': exec_sed_doc,
         'transposeVcmlCsv': transpose_vcml_csv,
+        'genPlotPdfs': gen_plot_pdfs,
     })