Skip to content

Commit

Permalink
Merge pull request #141 from JannisHoch/update_docs
Browse files Browse the repository at this point in the history 
now working for specific IDs or entire area
  • Loading branch information
@JannisHoch
JannisHoch committed Jun 4, 2021
2 parents 4f70e54 + 9c38a19 commit 347d20e
Showing 1 changed file with 53 additions and 31 deletions.
84 changes: 53 additions & 31 deletions copro/scripts/postprocessing/plot_value_over_time.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,39 +18,46 @@ def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=No
"""Quick and dirty function to plot the develoment of a column in the outputted geojson-files over time.
"""

click.echo(polygon_id)
click.echo('\nPLOTTING VARIABLE DEVELOPMENT OVER TIME')

assert(len(polygon_id) > 0), AssertionError('please specify at least one polygon ID to be sampled or select ''all'' for sampling the entire study area')
# converting polygon IDs to list
polygon_id = list(polygon_id)

# check that there is at least one ID or 'all' specified
assert(len(polygon_id) > 0), AssertionError('ERROR: please specify at least one polygon ID to be sampled or select ''all'' for sampling the entire study area')

# if 'all' is specified, no need to have list but get value directly
if polygon_id[0] == 'all':
click.echo('INFO: selected entire study area')
polygon_id = 'all'

# absolute path to input_dir
input_dir = os.path.abspath(input_dir)
click.echo('\ngetting geojson-files from {}'.format(input_dir))
click.echo('INFO: getting geojson-files from {}'.format(input_dir))

# collect all files in input_dir
all_files = glob.glob(os.path.join(input_dir, '*.geojson'))

if verbose:
if verbose:
if polygon_id != 'all':
click.echo('sampling from IDs'.format(polygon_id))
else:
click.echo('sampling over entire study area')
click.echo('DEBUG: sampling from IDs'.format(polygon_id))

# create dictionary with list for areas (either IDs or entire study area) to be sampled from
out_dict = dict()
for idx in polygon_id:
if polygon_id != 'all':
out_dict[int(idx)] = list()
else:
out_dict[idx] = list()
if polygon_id != 'all':
for idx in polygon_id:
out_dict[int(idx)] = list()
else:
out_dict[polygon_id] = list()

# create a list to keep track of year-values in files
years = list()

# go through all files
click.echo('retrieving values from column {}'.format(column))
click.echo('INFO: retrieving values from column {}'.format(column))
for geojson in all_files:

if verbose: click.echo('reading file {}'.format(geojson))
if verbose: click.echo('DEBUG: reading file {}'.format(geojson))
# read file and convert to geo-dataframe
gdf = gpd.read_file(geojson, driver='GeoJSON')
# convert geo-dataframe to dataframe
Expand All @@ -60,30 +67,29 @@ def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=No
year = int(str(str(os.path.basename(geojson)).rsplit('.')[0]).rsplit('_')[-1])
years.append(year)

# go throough all IDs
if polygon_id != 'all':
# go throough all IDs
for idx in polygon_id:
if verbose:
if polygon_id != 'all':
print('sampling ID {}'.format(idx))
click.echo('DEBUG: sampling ID {}'.format(idx))

# if ID not in file, assign NaN
if idx not in df.ID.values:
print('WARNING: ID {} is not in {} - NaN set'.format(idx, geojson))
if int(idx) not in df.ID.values:
click.echo('WARNING: ID {} is not in {} - NaN set'.format(int(idx), geojson))
vals = np.nan
# otherwise, get value of column at this ID
else:
vals = df[column].loc[df.ID==idx].values[0]
vals = df[column].loc[df.ID==int(idx)].values[0]

# append this value to list in dict
idx_list = out_dict[idx]
idx_list = out_dict[int(idx)]
idx_list.append(vals)

else:
# compute mean value over column
vals = df[column].mean()
# append this value to list in dict
idx_list = out_dict[idx]
idx_list = out_dict[polygon_id]
idx_list.append(vals)


Expand All @@ -94,21 +100,37 @@ def main(input_dir=None, polygon_id=None, column=None, title=None, output_dir=No

# create an output folder, if not yet there
if not os.path.isdir(os.path.abspath(output_dir)):
click.echo('creating output folder {}'.format(os.path.abspath(output_dir)))
click.echo('INFO: creating output folder {}'.format(os.path.abspath(output_dir)))
os.makedirs(os.path.abspath(output_dir))

# save dataframe as csv-file
df.to_csv(os.path.abspath(os.path.join(output_dir, '{}_dev.csv'.format(column))))
if polygon_id != 'all':
click.echo('INFO: saving to file {}'.format(os.path.abspath(os.path.join(output_dir, '{}_dev_IDs.csv'.format(column)))))
df.to_csv(os.path.abspath(os.path.join(output_dir, '{}_dev_IDs.csv'.format(column))))
else:
click.echo('INFO: saving to file {}'.format(os.path.abspath(os.path.join(output_dir, '{}_dev_all.csv'.format(column)))))
df.to_csv(os.path.abspath(os.path.join(output_dir, '{}_dev_all.csv'.format(column))))

# create a simple plot and save to file
fig, axes = plt.subplots(nrows=len(polygon_id), ncols=1, sharex=True)
df.plot(subplots=True, ax=axes)
for ax in axes:
# if IDs are specified, with one subplot per ID
if polygon_id != 'all':
fig, axes = plt.subplots(nrows=len(polygon_id), ncols=1, sharex=True)
df.plot(subplots=True, ax=axes)
for ax in axes:
ax.set_ylim(0, 1)
ax.set_yticks(np.arange(0, 1.1, 1))
if title != None:
ax.set_title(str(title))
plt.savefig(os.path.abspath(os.path.join(output_dir, '{}_dev_IDs.png'.format(column))), dpi=300, bbox_inches='tight')
# otherwise, only one plot needed
else:
fig, ax = plt.subplots(nrows=1, ncols=1, sharex=True)
df.plot(ax=ax)
ax.set_ylim(0, 1)
ax.set_yticks(np.arange(0, 1.1, 1))
if title != None:
ax.set_title(str(title))
plt.savefig(os.path.abspath(os.path.join(output_dir, '{}_dev.png'.format(column))), dpi=300, bbox_inches='tight')
if title != None:
ax.set_title(str(title))
plt.savefig(os.path.abspath(os.path.join(output_dir, '{}_dev_all.png'.format(column))), dpi=300, bbox_inches='tight')

if __name__ == '__main__':

Expand Down

0 comments on commit 347d20e

Please sign in to comment.