Merge pull request #113 from ACME-Climate/save_metrics

Save metrics

acme_diags/__init__.py

@@ -1,2 +1 @@
-
-__version__ = 'v1.0.0'
+__version__ = 'v1.1.0'

acme_diags/acme_diags_driver.py

@@ -11,6 +11,9 @@
 from acme_diags.acme_parser import ACMEParser
 from acme_diags.acme_viewer import create_viewer
 from acme_diags.driver.utils import get_set_name
+import json
+import collections
+import csv
 
 
 def _get_default_diags(set_num, dataset):
@@ -131,5 +134,6 @@ def run_diag(parameters):
             os.makedirs(pth)
 
         create_viewer(pth, parameters, parameters[0].output_format[0])
+
     else:
         print('There was not a single valid diagnostics run, no viewer created')

acme_diags/acme_viewer.py

@@ -4,9 +4,12 @@
 import datetime
 import shutil
 import collections
+import copy
+import csv
+import json
 from bs4 import BeautifulSoup
-import acme_diags
 from cdp.cdp_viewer import OutputViewer
+import acme_diags
 from acme_diags.driver.utils import get_set_name
 
 # Dict of
@@ -24,6 +27,8 @@
 # needed so we can have a cols in order of ANN, DJF, MAM, JJA, SON
 ROW_INFO = collections.OrderedDict()
 
+# A similar dict for creating the lat-lon tables
+LAT_LON_TABLE_INFO = collections.OrderedDict()
 
 def _copy_acme_logo(root_dir):
     """Copy over ACME_Logo.png to root_dir/viewer"""
@@ -127,7 +132,10 @@ def _extras(root_dir, parameters):
                     parameters[0].test_name, dt, path)
         h1_to_h3(f)
 
+    _edit_table_html(root_dir)
+    _add_lat_lon_table_to_viewer_index(root_dir)
 
+
 def _add_pages_and_top_row(viewer, parameters):
     """Add the page and columns of the page"""
     set_to_seasons = collections.OrderedDict()  # dict of {set: [seasons]}
@@ -169,7 +177,163 @@ def _better_page_name(old_name):
         return 'CloudTopHeight-Tau joint histograms'
     else:
         return old_name
+
+def _add_to_lat_lon_metrics_table(metrics_path, season, row_name):
+    """Add the metrics for the current season and row_name to the lat-lon table"""
+    with open(metrics_path + '.json') as json_file:
+        metrics_dict = json.load(json_file)
+
+        if season not in LAT_LON_TABLE_INFO:
+            LAT_LON_TABLE_INFO[season] = collections.OrderedDict()
+        if row_name not in LAT_LON_TABLE_INFO[season]:
+            LAT_LON_TABLE_INFO[season][row_name] = collections.OrderedDict()
+        LAT_LON_TABLE_INFO[season][row_name]['metrics'] = metrics_dict
+
+def _create_csv_from_dict(output_dir, season):
+    """Create a csv for a season in LAT_LON_TABLE_INFO in output_dir and return the path to it"""
+    #table_path = os.path.abspath(os.path.join(output_dir, season + '_metrics_table.csv'))
+    table_path = os.path.join(output_dir, season + '_metrics_table.csv')
+
+    col_names = ['Variables', 'Unit', 'Model mean', 'Obs mean', 'Mean Bias', 'RMSE', 'correlation']
+
+    with open(table_path, 'w') as table_csv:
+        writer=csv.writer(table_csv, delimiter=',', lineterminator='\n', quoting=csv.QUOTE_NONE)
+        writer.writerow(col_names)
+        for key, metrics_dic in LAT_LON_TABLE_INFO[season].items():
+            metrics = metrics_dic['metrics']
+            row = [key, metrics['unit'], round(metrics['test_regrid']['mean'],3), round(metrics['ref_regrid']['mean'],3), round(metrics['test_regrid']['mean'] - metrics['ref_regrid']['mean'],3), round(metrics['misc']['rmse'],3), round(metrics['misc']['corr'],3)]
+            writer.writerow(row)
+
+    return table_path
+
+def _cvs_to_html(csv_path, season):
+    """Convert the csv for a season located at csv_path to an HTML, returning the path to the HTML"""
+    html_path = csv_path.replace('csv', 'html')
+
+    with open(html_path, 'w') as htmlfile:
+        htmlfile.write('<p><th><b>{} Mean </b></th></p>'.format(season))
+        htmlfile.write('<table>')
+
+        with open(csv_path) as csv_file:
+            read_csv = csv.reader(csv_file)
+
+            # generate table contents
+            for num, row in enumerate(read_csv):
+
+                # write the header row, assuming the first row in csv contains the header
+                if num == 0:
+                    htmlfile.write('<tr>')
+                    for column in row:
+                        htmlfile.write('<th>{}</th>'.format(column))
+                    htmlfile.write('</tr>')
+
+                # write all other rows 
+                else:
+                    htmlfile.write('<tr><div style="width: 50px">')
+                    for column in row:
+                        htmlfile.write('<td>{}</td>'.format(column))
+                    htmlfile.write('</div></tr>')
+
+        htmlfile.write('</table>')
+
+    return html_path
+
+
+def _add_html_to_col(season, season_path, html_path):
+    """Since the output viewer doesn't support html images, do this hack.
+    For the col in the html at html_path, insert the link to col_path."""
+    # Change:
+    # <tr class="output-row">
+    #  <!-- ... -->
+    #  <td colspan="1">
+    #   <!-- what needs to be changed -->
+    #  </td>
+    # <!-- ... -->
+    # </tr>
+    # to:
+    # <tr class="output-row">
+    #  <!-- ... -->
+    #  <td colspan="1">
+    #   <a href="{season_path}"> {season} </a> <!-- this was changed -->
+    #  </td>
+    # <!-- ... -->
+    # </tr>
+
+    soup = BeautifulSoup(open(html_path), "lxml")
+
+    for tr in soup.find_all("tr", {"class": "output-row"}):
+        index = ['All variables', 'ANN', 'DJF', 'MAM', 'JJA', 'SON'].index(season)
+        cols = tr.find_all("td")  # the cols are ['All variables', 'ANN', 'DJF', 'MAM', 'JJA', 'SON']
+        td = cols[index]  # get the HTML element related to the season
+
+        url = os.path.join('..', '..', '..', season_path)
+        a = soup.new_tag("a", href=url)
+        a.append(season)
+
+        td.string = ''
+        td.append(a)
+
+    html = soup.prettify("utf-8")
+    with open(html_path, "wb") as f:
+        f.write(html)
+
+def _edit_table_html(root_dir):
+    """After the viewer is created, edit the table html to insert the custom htmls"""
+    for s in ['ANN', 'DJF', 'MAM', 'JJA', 'SON']:
+        if s in LAT_LON_TABLE_INFO:
+            _add_html_to_col(s, LAT_LON_TABLE_INFO[s]['html_path'], os.path.join(root_dir, 'table', 'index.html'))
+
+def _create_lat_lon_table_index(viewer, root_dir):
+    """Create an index in the viewer that links the individual htmls for the lat-lon table."""
+    seasons = ['ANN', 'DJF', 'MAM', 'JJA', 'SON']
+    viewer.add_page('Table', seasons)
+    viewer.add_group('Summary Table')
+    viewer.add_row('All variables')
+
+    for s in seasons:
+        if s in LAT_LON_TABLE_INFO:
+            viewer.add_col(LAT_LON_TABLE_INFO[s]['html_path'], is_file=False, title=s)
+        else:
+            viewer.add_col('-----', is_file=True, title='-----')
+
+def _add_lat_lon_table_to_viewer_index(root_dir):
+    """Move the link to Table next to the link to Latitude-Longitude contour maps"""
+    index_page = os.path.join(root_dir, 'index.html')
+    soup = BeautifulSoup(open(index_page), "lxml")
+
+    # append the new tag underneath the old one, so add it to the parent of the old one
+    td_to_move = None
+    for tr in soup.find_all("tr"):
+        for td in tr.find_all("td"):
+            for a in td.find_all("a"):
+                if 'table' in a['href']:
+                    td_to_move = copy.deepcopy(td)
+                    tr.decompose()
+
+    if td_to_move:
+        for tr in soup.find_all("tr"):
+            for td in tr.find_all("td"):
+                for a in td.find_all("a"):
+                    if _better_page_name('lat_lon') in a.string:
+                        td.append(td_to_move)
+
+    html = soup.prettify("utf-8")
+    with open(index_page, "wb") as f:
+        f.write(html)
+
+def generate_lat_lon_metrics_table(viewer, root_dir):
+    """For each season in LAT_LON_TABLE_INFO, create a csv, convert it to an html and append that html to the viewer."""
+    table_dir = os.path.join(root_dir, 'table-data')  # output_dir/viewer/table-data
+
+    if not os.path.exists(table_dir):
+        os.mkdir(table_dir)
+
+    for season in LAT_LON_TABLE_INFO:
+        csv_path = _create_csv_from_dict(table_dir, season)
+        html_path = _cvs_to_html(csv_path, season)
+        LAT_LON_TABLE_INFO[season]['html_path'] = html_path
 
+    _create_lat_lon_table_index(viewer, root_dir)
 
 def create_viewer(root_dir, parameters, ext):
     """Based of the parameters, find the files with
@@ -207,6 +371,13 @@ def create_viewer(root_dir, parameters, ext):
                                     ref_name, var, int(plev), season, region)
                                 row_name_and_fnm.append((row_name, fnm))
 
+                        if set_num in ['lat_lon', '5']:
+                            metrics_path = os.path.join(parameter.results_dir, '{}'.format(set_num), parameter.case_id, fnm)
+                            if os.path.exists(metrics_path + '.json'):
+                                _add_to_lat_lon_metrics_table(metrics_path, season, row_name)
+                            else:
+                                print('JSON does not exist: {}'.format(metrics_path + '.json'))
+                                continue
                         for row_name, fnm in row_name_and_fnm:
                             if parameter.case_id not in ROW_INFO[set_num]:
                                 ROW_INFO[set_num][parameter.case_id] = collections.OrderedDict(
@@ -255,5 +426,6 @@ def create_viewer(root_dir, parameters, ext):
                         viewer.add_col(fnm + '.' + ext, is_file=True,
                                        title=col_season, other_files=formatted_files)
 
+    generate_lat_lon_metrics_table(viewer, root_dir)
     viewer.generate_viewer(prompt_user=False)
     _extras(root_dir, parameters)

acme_diags/driver/lat_lon_driver.py

@@ -6,34 +6,44 @@
 from acme_diags.derivations import acme
 from acme_diags.metrics import rmse, corr, min_cdms, max_cdms, mean
 from acme_diags.driver import utils
+from acme_diags.driver.utils import get_output_dir
 import os
 import sys
+import json
 
 
 def create_metrics(ref, test, ref_regrid, test_regrid, diff):
     """Creates the mean, max, min, rmse, corr in a dictionary"""
     metrics_dict = {}
     metrics_dict['ref'] = {
-        'min': min_cdms(ref),
-        'max': max_cdms(ref),
-        'mean': mean(ref)
+        'min': float(min_cdms(ref)),
+        'max': float(max_cdms(ref)),
+        'mean': float(mean(ref))
+    }
+    metrics_dict['ref_regrid'] = {
+        'min': float(min_cdms(ref_regrid)),
+        'max': float(max_cdms(ref_regrid)),
+        'mean': float(mean(ref_regrid))
     }
     metrics_dict['test'] = {
-        'min': min_cdms(test),
-        'max': max_cdms(test),
-        'mean': mean(test)
+        'min': float(min_cdms(test)),
+        'max': float(max_cdms(test)),
+        'mean': float(mean(test))
+    }
+    metrics_dict['test_regrid'] = {
+        'min': float(min_cdms(test_regrid)),
+        'max': float(max_cdms(test_regrid)),
+        'mean': float(mean(test_regrid))
     }
-
     metrics_dict['diff'] = {
-        'min': min_cdms(diff),
-        'max': max_cdms(diff),
-        'mean': mean(diff)
+        'min': float(min_cdms(diff)),
+        'max': float(max_cdms(diff)),
+        'mean': float(mean(diff))
     }
     metrics_dict['misc'] = {
-        'rmse': rmse(test_regrid, ref_regrid),
-        'corr': corr(test_regrid, ref_regrid)
+        'rmse': float(rmse(test_regrid, ref_regrid)),
+        'corr': float(corr(test_regrid, ref_regrid))
     }
-
     return metrics_dict
 
 
@@ -184,6 +194,14 @@ def run_diag(parameter):
                         metrics_dict = create_metrics(
                             mv2_domain, mv1_domain, mv2_reg, mv1_reg, diff)
 
+                        metrics_dict['unit'] = mv1_reg.units
+
+                        fnm = os.path.join(get_output_dir(
+                            parameter.current_set, parameter), parameter.output_file)
+                        with open(fnm + '.json' , 'w') as outfile:
+                             json.dump(metrics_dict,outfile)
+                        print('Metrics saved in: ' + fnm + '.json')
+
                         parameter.var_region = region
                         plot(parameter.current_set, mv2_domain,
                              mv1_domain, diff, metrics_dict, parameter)
@@ -232,6 +250,15 @@ def run_diag(parameter):
                     diff = mv1_reg - mv2_reg
                     metrics_dict = create_metrics(
                         mv2_domain, mv1_domain, mv2_reg, mv1_reg, diff)
+
+                    metrics_dict['unit'] = mv1_reg.units
+
+                    fnm = os.path.join(get_output_dir(
+                        parameter.current_set, parameter), parameter.output_file)
+                    with open(fnm + '.json' , 'w') as outfile:
+                         json.dump(metrics_dict,outfile)
+                    print('Metrics saved in: ' + fnm + '.json')
+
                     parameter.var_region = region
                     plot(parameter.current_set, mv2_domain,
                          mv1_domain, diff, metrics_dict, parameter)