Merge pull request #123 from valeriupredoi/dev_dpi

Added dpi and savepdf options to comparison report for publications

README.md

@@ -226,6 +226,8 @@ do_mass_download: <bool>
 master_suites: <str>
 auto_download: <bool>
 strictFileCheck: <bool>
+dpi: <int>
+savepdf: <bool>
 
 jobs:
    <jobID1>:
@@ -268,6 +270,15 @@ These values are:
  - `strictFileCheck`: 
    - A boolean which when True will raise an error if input model files are missing. 
    - Default is True, set to False to skip this check.
+ - `dpi`:
+   - The resolution in dots per inch (dpi) of the output image.
+   - dpi=100 is fine for most purposes but 300 is needed for highres posters/publications.
+   - If set to `None`, then the dpi will be set to your default value.
+ - `savepdf`:
+   - Output the image as a pdf in addition to the standard png. 
+   - This doesn't replace the image in the report, but saves a pdf version of the image in the images directory.
+   - The pdfs will be web-visible in the report image directory, but will not linked in the html.
+   - To view a pdf from a report, simply click the image, and replace the `png` extension with `pdf` in the browser path. 
  - `jobs`:
    - A list of jobIDs, and some options on how they will appear in the final report.
    - The options are:

bgcval2/analysis_compare.py

@@ -192,6 +192,8 @@ def timeseries_compare(jobs,
                        labels = {},
                        ensembles={},
                        config_user=None,
+                       dpi=None,
+                       savepdf=False,
     ):
     """
     timeseries_compare:
@@ -423,6 +425,8 @@ def timeseries_compare(jobs,
                     thicknesses=lineThicknesses,
                     linestyles=linestyles,
                     labels=labels,
+                    dpi=dpi,
+                    savepdf=savepdf,
                 )
 
     # Generate a list of comparison images:
@@ -504,6 +508,19 @@ def load_comparison_yml(master_compare_yml_fn):
     details['do_mass_download'] = input_yml_dict.get('do_mass_download', False)
     details['master_suites'] = input_yml_dict.get('master_suites', [])
 
+    # Image output settings:
+    # dpi: pixels per inch (image resolution)
+    # savepdf: also save the image as a pdf. 
+    details['dpi'] = input_yml_dict.get('dpi', None)
+    details['savepdf'] = input_yml_dict.get('savepdf', False)
+
+    if details['dpi']: # None is valid!
+        try: 
+            int(details['dpi']) 
+        except: 
+            raise ValueError(''.join(["Loading yml error: `dpi` needs to be an integer. Current value:",
+                                      str(details['dpi'])]))
+
     # auto download, can differ for each job.
     auto_download = input_yml_dict.get('auto_download', True)
     auto_download_dict = {jobID: auto_download for jobID in details['jobs'].keys()}
@@ -579,6 +596,9 @@ def load_yml_and_run(compare_yml, config_user, skip_timeseries):
     suites = details['suites']
     auto_download = details['auto_download']
     strictFileCheck = details.get('strictFileCheck', True)
+    dpi = details.get('dpi', None)
+    savepdf = details.get('savepdf', False)
+
     print('---------------------')
     print('timeseries_compare:',  analysis_name)
     print('job ids:', jobs.keys())
@@ -632,6 +652,9 @@ def load_yml_and_run(compare_yml, config_user, skip_timeseries):
         linestyles=linestyles,
         labels=labels,
         config_user=config_user,
+        dpi=dpi,
+        savepdf=savepdf,
+
     )
 
 

bgcval2/bgcval2_make_report.py

@@ -81,26 +81,42 @@ def addImageToHtml(fn, imagesfold, reportdir, debug=True):
             "\n\tnewfn:", newfn,
             "\n\trelfn:", relfn)
 
-
+    # sending a pdf as well.
+    pdf_fn = fn.replace('.png', '.pdf')
+    if os.path.exists(pdf_fn):
+        new_pdf_fn = newfn.replace('.png', '.pdf')
+        # Check if file is newer than the one in images.
+        if shouldIMakeFile(
+                pdf_fn,
+                new_pdf_fn,
+        ):
+            if debug:
+                print("addImageToHtml:\tAdding new pdf to report.", new_pdf_fn)
+            if os.path.exists(new_pdf_fn):
+                os.remove(new_pdf_fn)
+            shutil.copy2(pdf_fn, new_pdf_fn)
+
     if not os.path.exists(newfn):
-        if debug: print("addImageToHtml:\tcopytree", fn, newfn)
+        if debug: 
+            print("addImageToHtml:\tcopytree", fn, newfn)
         basedir = folder(os.path.dirname(newfn))
-        #copytree(fn, newfn)
         if os.path.isdir(fn):
             shutil.copytree(fn, newfn, symlinks, ignore)
         else:
             shutil.copy2(fn, newfn)
     else:
         ####
         # Check if the newer file is the same one from images.
-        if os.path.getmtime(fn) == os.path.getmtime(newfn): return relfn
+        if os.path.getmtime(fn) == os.path.getmtime(newfn): 
+            return relfn
         ####
         # Check if file is newer than the one in images.
         if shouldIMakeFile(
                 fn,
                 newfn,
         ):
-            if debug: print("addImageToHtml:\tremoving old file", fn)
+            if debug: 
+                print("addImageToHtml:\tremoving old file", fn)
             os.remove(newfn)
             shutil.copy2(fn, newfn)
             if debug: 
@@ -1636,7 +1652,6 @@ def newImageLocation(fn):
 
         if len(otherFilenames):
             # I think this is never happens anymore.
-            assert 0
             href = 'OtherPlots-others'
 
             hrefs.append(href)

bgcval2/timeseries/timeseriesPlots.py

@@ -35,6 +35,8 @@
 import matplotlib.patches as mpatches
 import cartopy
 import numpy as np
+import pathlib
+
 from numpy import hanning, hamming, bartlett, blackman
 from scipy import interpolate
 from collections import defaultdict
@@ -706,6 +708,8 @@ def multitimeseries(
         thicknesses=defaultdict(lambda: 1),
         linestyles=defaultdict(lambda: '-'),
         labels={},
+        dpi=None,
+        savepdf=False,
 ):
 
     if 0 in [len(timesD), len(list(timesD.keys()))]: return
@@ -1053,7 +1057,16 @@ def multitimeseries(
         pyplot.suptitle(title)
 
     print("multitimeseries:\tsimpletimeseries:\tSaving:", filename)
-    pyplot.savefig(filename)
+    if not dpi:
+        pyplot.savefig(filename)
+    imext = pathlib.Path(filename).suffix
+
+    # save image as pdf (publication?)
+    if savepdf:
+        pyplot.savefig(filename.replace(imext, '.pdf'))
+
+    if pathlib.Path(filename).suffix in ['.png', '.jpg', '.jpeg']:
+        pyplot.savefig(filename, dpi=dpi)
     pyplot.close()
 
 

input_yml/TerraFIRMA_overshoot_runs_minimal.yml

@@ -16,6 +16,9 @@ strict_file_check: False
 
 clean: True
 
+dpi: 300
+savepdf: True
+
 jobs:
     u-cs495:
        description: 'PI-Control'