Skip to content

version updates and revisions to make examples functional #102

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
pgbrodrick wants to merge 1 commit into
base: master
Choose a base branch
from
Open

version updates and revisions to make examples functional #102

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion environment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,5 +15,7 @@ dependencies:
- scikit-learn>=0.21.2
- scipy>=1.2.1
- shapely>=1.6.4
- tensorflow=1.13.1
- tensorflow=1.15
- tqdm>=4.32.1
- albumentations>=0.5.0
- requests
23 changes: 11 additions & 12 deletions examples/flight_line_extrapolation/flight_line_extrapolation_example.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
import argparse
import os

import rsCNN.reporting.reports
from rsCNN.configuration import configs
from rsCNN.data_management import apply_model_to_data, data_core
from rsCNN.experiments import experiments
from rsCNN.utils import logging
import bfgn.reporting.reports
from bfgn.configuration import configs
from bfgn.data_management import apply_model_to_data, data_core
from bfgn.experiments import experiments
from bfgn.utils import logging

parser = argparse.ArgumentParser(description='Example spatial extrapolation application')
parser.add_argument('settings_file')
Expand All @@ -14,8 +14,8 @@
parser.add_argument('-debug_file', type=str, default='debug.out')
args = parser.parse_args()

logger = logging.get_root_logger(args.debug_file)
logger.setLevel(args.debug_level)
if args.debug_file is not None:
logger = logging.get_bfgn_logger(None, args.debug_level, args.debug_file)

assert os.path.isfile(args.settings_file), 'Settings file: ' + args.settings_file + ' does not exist'
config = configs.create_config_from_file(args.settings_file)
Expand All @@ -30,23 +30,22 @@
experiment.build_or_load_model(data_container=data_container)

if (args.key == 'prelim_report'):
prelim_report = rsCNN.reporting.reports.Reporter(data_container, experiment, config)
prelim_report = bfgn.reporting.reports.Reporter(data_container, experiment, config)
prelim_report.create_model_report()

if (args.key == 'train' or args.key == 'all'):
experiment.fit_model_with_data_container(data_container, resume_training=True)

if (args.key == 'report' or args.key == 'all'):
final_report = rsCNN.reporting.reports.Reporter(data_container, experiment, config)
final_report = bfgn.reporting.reports.Reporter(data_container, experiment, config)
final_report.create_model_report()

if (args.key == 'apply' or args.key == 'all'):
application_feature_files = config.raw_files.feature_files[0]
application_output_basenames = ['examples/output/feat_subset_applied_cnn.tif']
for _f in range(len(application_feature_files)):
rsCNN.data_management.apply_model_to_data.apply_model_to_raster(experiment.model,
bfgn.data_management.apply_model_to_data.apply_model_to_site(experiment.model,
data_container,
application_feature_files[_f],
application_output_basenames[_f],
make_png=False,
make_tif=True)
output_format="GTiff")
52 changes: 29 additions & 23 deletions examples/termite_mounds/termite_mound_example.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,21 +8,21 @@
import gdal
import requests

import rsCNN.reporting.reports
from rsCNN.configuration import configs
from rsCNN.data_management import apply_model_to_data, data_core
from rsCNN.experiments import experiments
from rsCNN.utils import logging
import bfgn.reporting.reports
from bfgn.configuration import configs
from bfgn.data_management import apply_model_to_data, data_core
from bfgn.experiments import experiments
from bfgn.utils import logging

parser = argparse.ArgumentParser(description='Example termite mound classification')
parser.add_argument('key', type=str, choices=['all', 'prelim_report', 'train', 'report', 'apply'])
parser.add_argument('-debug_level', type=str, default='INFO', choices=['DEBUG', 'INFO', 'WARN', 'ERROR'])
parser.add_argument('-debug_file', type=str, default='debug.out')
parser.add_argument('-debug_file', type=str, default=None)
parser.add_argument('-run_as_raster', type=bool, default=False)
args = parser.parse_args()

logger = logging.get_root_logger(args.debug_file)
logger.setLevel(args.debug_level)

if args.debug_file is not None:
logger = logging.get_bfgn_logger(None, args.debug_level, args.debug_file)

######################### Download sample data from ecoCNN ################################
DATA_DIR = 'scratch'
Expand Down Expand Up @@ -86,17 +86,23 @@ def get_data_from_url(url, destination):
experiment = experiments.Experiment(config)
experiment.build_or_load_model(data_container=data_container)

experiment.fit_model_with_data_container(data_container, resume_training=True)

final_report = rsCNN.reporting.reports.Reporter(data_container, experiment, config)
final_report.create_model_report()

application_feature_files = config.raw_files.feature_files[0]
application_output_basenames = ['scratch/applied_output_model.tif']
for _f in range(len(application_feature_files)):
rsCNN.data_management.apply_model_to_data.apply_model_to_raster(experiment.model,
data_container,
application_feature_files[_f],
application_output_basenames[_f],
make_png=True,
make_tif=True)
if (args.key == 'prelim_report' or args.key == 'all'):
prelim_report = bfgn.reporting.reports.Reporter(data_container, experiment, config)
prelim_report.create_model_report()

if (args.key == 'train' or args.key == 'all'):
experiment.fit_model_with_data_container(data_container, resume_training=True)

if (args.key == 'report' or args.key == 'all'):
final_report = bfgn.reporting.reports.Reporter(data_container, experiment, config)
final_report.create_model_report()

if (args.key == 'apply' or args.key == 'all'):
application_feature_files = config.raw_files.feature_files[0]
application_output_basenames = ['scratch/applied_output_model']
for _f in range(len(application_feature_files)):
bfgn.data_management.apply_model_to_data.apply_model_to_site(experiment.model,
data_container,
[application_feature_files[_f]],
application_output_basenames[_f],
output_format="GTiff")