def process_message(self, connector, host, secret_key, resource,
parameters):
self.start_message(resource)
f = resource['local_paths'][0]
self.log_info(resource, "determining image quality")
qual = getImageQuality(f)
self.log_info(resource, "creating output image")
md = download_ds_metadata(connector, host, secret_key,
resource['parent']['id'])
terramd = get_terraref_metadata(md)
if "left" in f:
bounds = geojson_to_tuples(
terramd['spatial_metadata']['left']['bounding_box'])
else:
bounds = geojson_to_tuples(
terramd['spatial_metadata']['right']['bounding_box'])
output = f.replace(".tif", "_nrmac.tif")
create_geotiff(np.array([[qual, qual], [qual, qual]]), bounds, output)
upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, resource['parent']['id'], output)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
ext_meta = build_metadata(host, self.extractor_info, resource['id'],
{"quality_score": qual}, 'file')
self.log_info(resource, "uploading extractor metadata")
upload_metadata(connector, host, secret_key, resource['id'], ext_meta)
self.end_message(resource)
def flir2tif(input_paths, full_md=None):
# Determine metadata and BIN file
bin_file = None
for f in input_paths:
if f.endswith(".bin"):
bin_file = f
if f.endswith("_cleaned.json") and full_md is None:
with open(f, 'r') as mdf:
full_md = json.load(mdf)['content']
# TODO: Figure out how to pass extractor details to create_geotiff in both types of pipelines
extractor_info = None
if full_md:
if bin_file is not None:
out_file = bin_file.replace(".bin", ".tif")
gps_bounds_bin = geojson_to_tuples(
full_md['spatial_metadata']['flirIrCamera']['bounding_box'])
raw_data = np.fromfile(bin_file,
np.dtype('<u2')).reshape([480, 640
]).astype('float')
raw_data = np.rot90(raw_data, 3)
tc = rawData_to_temperature(raw_data, full_md)
create_geotiff(tc,
gps_bounds_bin,
out_file,
None,
False,
extractor_info,
full_md,
compress=True)
# Return formatted dict for simple extractor
return {"metadata": {"files_created": [out_file]}, "outputs": [out_file]}
def do_work(left_file, right_file, json_file):
"""Make the calls to convert the files
Args:
left_file(str): Path to the left BIN file
right_file(str): Path to the right BIN file
json_file(str): Path to the JSON file
"""
out_left = os.path.splitext(left_file)[0] + ".tif"
out_right = os.path.splitext(right_file)[0] + ".tif"
file_name, file_ext = os.path.splitext(json_file)
out_json = file_name + "_updated" + file_ext
# Load the JSON
with open(json_file, "r") as infile:
metadata = json.load(infile)
if not metadata:
raise RuntimeError("JSON file appears to be invalid: " + json_file)
md_len = len(metadata)
if md_len <= 0:
raise RuntimeError("JSON file is empty: " + json_file)
# Prepare the metadata
clean_md = get_terraref_metadata(clean_metadata(metadata, 'stereoTop'), 'stereoTop')
# Pull out the information we need from the JSON
try:
left_shape = terraref.stereo_rgb.get_image_shape(clean_md, 'left')
gps_bounds_left = geojson_to_tuples(clean_md['spatial_metadata']['left']['bounding_box'])
right_shape = terraref.stereo_rgb.get_image_shape(clean_md, 'right')
gps_bounds_right = geojson_to_tuples(clean_md['spatial_metadata']['right']['bounding_box'])
except KeyError:
print("ERROR: Spatial metadata not properly identified in JSON file")
return
# Make the conversion calls
print("creating %s" % out_left)
left_image = terraref.stereo_rgb.process_raw(left_shape, left_file, None)
create_geotiff(left_image, gps_bounds_left, out_left, asfloat=False, system_md=clean_md, compress=False)
print("creating %s" % out_right)
right_image = terraref.stereo_rgb.process_raw(right_shape, right_file, None)
create_geotiff(right_image, gps_bounds_right, out_right, asfloat=False, system_md=clean_md, compress=True)
# Write the metadata
print("creating %s" % out_json)
with open(out_json, "w") as outfile:
json.dump(clean_md, outfile, indent=4)
def process_message_individual(self, connector, host, secret_key, resource,
parameters):
"""This is deprecated method that operates on single capture, not field mosaic"""
self.start_message()
input_image = resource['local_paths'][0]
# Create output in same directory as input, but check name
ds_md = get_info(connector, host, secret_key, resource['parent']['id'])
terra_md = get_terraref_metadata(
download_metadata(connector, host, secret_key,
resource['parent']['id']), 'stereoTop')
dataset_name = ds_md['name']
timestamp = dataset_name.split(" - ")[1]
# Is this left or right half?
side = 'left' if resource['name'].find("_left") > -1 else 'right'
gps_bounds = geojson_to_tuples(
terra_md['spatial_metadata'][side]['bounding_box'])
out_csv = self.sensors.create_sensor_path(timestamp,
opts=[side],
ext='csv')
out_dgci = out_csv.replace(".csv", "_dgci.png")
out_edge = out_csv.replace(".csv", "_edge.png")
out_label = out_csv.replace(".csv", "_label.png")
out_dgci_tif = out_dgci.replace('.png', '.tif')
out_edge_tif = out_edge.replace('.png', '.tif')
out_label_tif = out_label.replace('.png', '.tif')
self.generate_all_outputs(input_image, out_csv, out_dgci, out_edge,
out_label, gps_bounds)
fileids = []
for file_to_upload in [
out_csv, out_dgci_tif, out_edge_tif, out_label_tif
]:
if os.path.isfile(file_to_upload):
if file_to_upload not in resource['local_paths']:
# TODO: Should this be written to a separate dataset?
#target_dsid = build_dataset_hierarchy(connector, host, secret_key, self.clowderspace,
# self.sensors.get_display_name(),
# timestamp[:4], timestamp[5:7], timestamp[8:10], leaf_ds_name=dataset_name)
# Send output to Clowder source dataset
fileids.append(
upload_to_dataset(connector, host, secret_key,
resource['parent']['id'],
file_to_upload))
self.created += 1
self.bytes += os.path.getsize(file_to_upload)
# Add metadata to original dataset indicating this was run
ext_meta = build_metadata(host, self.extractor_info,
resource['parent']['id'],
{"files_created": fileids}, 'dataset')
upload_metadata(connector, host, secret_key, resource['parent']['id'],
ext_meta)
self.end_message()
def get_maskfilename_bounds(self, file_name, datestamp):
"""Determines the name of the masking file and loads the boundaries of the file
Args:
file_name(str): path of the file to create a mask from
datestamp(str): the date to use when creating file paths
Return:
"""
mask_name, bounds = (None, None)
if not self.get_terraref_metadata is None:
key = 'left' if file_name.endswith('_left.tif') else 'right'
mask_name = self.sensors.create_sensor_path(datestamp, opts=[key])
bounds = geojson_to_tuples(self.get_terraref_metadata['spatial_metadata'][key]['bounding_box'])
else:
mask_name = self.sensors.create_sensor_path(datestamp)
bounds = image_get_geobounds(file_name)
bounds_len = len(bounds)
if bounds_len <= 0 or bounds[0] == np.nan:
bounds = None
return (mask_name, bounds)
def process_message(self, connector, host, secret_key, resource, parameters):
self.start_message(resource)
# Get left/right files and metadata
img_left, img_right, terra_md_full = None, None, None
for fname in resource['local_paths']:
if fname.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(fname)
terra_md_full = get_terraref_metadata(all_dsmd, 'stereoTop')
elif fname.endswith('_left.bin'):
img_left = fname
elif fname.endswith('_right.bin'):
img_right = fname
if None in [img_left, img_right, terra_md_full]:
raise ValueError("could not locate all files & metadata in processing")
timestamp = resource['dataset_info']['name'].split(" - ")[1]
# Fetch experiment name from terra metadata
season_name, experiment_name, updated_experiment = get_season_and_experiment(timestamp, 'stereoTop', terra_md_full)
if None in [season_name, experiment_name]:
raise ValueError("season and experiment could not be determined")
# Determine output directory
self.log_info(resource, "Hierarchy: %s / %s / %s / %s / %s / %s / %s" % (season_name, experiment_name, self.sensors.get_display_name(),
timestamp[:4], timestamp[5:7], timestamp[8:10], timestamp))
target_dsid = build_dataset_hierarchy_crawl(host, secret_key, self.clowder_user, self.clowder_pass, self.clowderspace,
season_name, experiment_name, self.sensors.get_display_name(),
timestamp[:4], timestamp[5:7], timestamp[8:10],
leaf_ds_name=self.sensors.get_display_name() + ' - ' + timestamp)
left_tiff = self.sensors.create_sensor_path(timestamp, opts=['left'])
right_tiff = self.sensors.create_sensor_path(timestamp, opts=['right'])
uploaded_file_ids = []
# Attach LemnaTec source metadata to Level_1 product if necessary
target_md = download_metadata(connector, host, secret_key, target_dsid)
if not get_extractor_metadata(target_md, self.extractor_info['name']):
self.log_info(resource, "uploading LemnaTec metadata to ds [%s]" % target_dsid)
remove_metadata(connector, host, secret_key, target_dsid, self.extractor_info['name'])
terra_md_trim = get_terraref_metadata(all_dsmd)
if updated_experiment is not None:
terra_md_trim['experiment_metadata'] = updated_experiment
terra_md_trim['raw_data_source'] = host + ("" if host.endswith("/") else "/") + "datasets/" + resource['id']
level1_md = build_metadata(host, self.extractor_info, target_dsid, terra_md_trim, 'dataset')
upload_metadata(connector, host, secret_key, target_dsid, level1_md)
try:
left_shape = terraref.stereo_rgb.get_image_shape(terra_md_full, 'left')
gps_bounds_left = geojson_to_tuples(terra_md_full['spatial_metadata']['left']['bounding_box'])
right_shape = terraref.stereo_rgb.get_image_shape(terra_md_full, 'right')
gps_bounds_right = geojson_to_tuples(terra_md_full['spatial_metadata']['right']['bounding_box'])
except KeyError:
self.log_error(resource, "spatial metadata not properly identified; sending to cleaner")
submit_extraction(connector, host, secret_key, resource['id'], "terra.metadata.cleaner")
return
if (not file_exists(left_tiff)) or self.overwrite:
# Perform actual processing
self.log_info(resource, "creating %s" % left_tiff)
left_image = terraref.stereo_rgb.process_raw(left_shape, img_left, None)
create_geotiff(left_image, gps_bounds_left, left_tiff, None, True,
self.extractor_info, terra_md_full, compress=True)
self.created += 1
self.bytes += os.path.getsize(left_tiff)
# Check if the file should be uploaded, even if it was already created
found_in_dest = check_file_in_dataset(connector, host, secret_key, target_dsid, left_tiff)
if not found_in_dest:
self.log_info(resource, "uploading %s" % left_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user, self.clowder_pass, target_dsid, left_tiff)
uploaded_file_ids.append(host + ("" if host.endswith("/") else "/") + "files/" + fileid)
if (not file_exists(right_tiff)) or self.overwrite:
# Perform actual processing
self.log_info(resource, "creating %s" % right_tiff)
right_image = terraref.stereo_rgb.process_raw(right_shape, img_right, None)
create_geotiff(right_image, gps_bounds_right, right_tiff, None, True,
self.extractor_info, terra_md_full, compress=True)
self.created += 1
self.bytes += os.path.getsize(right_tiff)
# Check if the file should be uploaded, even if it was already created
found_in_dest = check_file_in_dataset(connector, host, secret_key, target_dsid, right_tiff)
if not found_in_dest:
self.log_info(resource, "uploading %s" % right_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user, self.clowder_pass, target_dsid, right_tiff)
uploaded_file_ids.append(host + ("" if host.endswith("/") else "/") + "files/" + fileid)
# Trigger additional extractors
self.log_info(resource, "triggering downstream extractors")
submit_extraction(connector, host, secret_key, target_dsid, "terra.stereo-rgb.rgbmask")
submit_extraction(connector, host, secret_key, target_dsid, "terra.stereo-rgb.nrmac")
submit_extraction(connector, host, secret_key, target_dsid, "terra.plotclipper_tif")
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
if len(uploaded_file_ids) > 0:
extractor_md = build_metadata(host, self.extractor_info, target_dsid, {
"files_created": uploaded_file_ids
}, 'dataset')
self.log_info(resource, "uploading extractor metadata to raw dataset")
remove_metadata(connector, host, secret_key, resource['id'], self.extractor_info['name'])
try:
upload_metadata(connector, host, secret_key, resource['id'], extractor_md)
except:
self.log_info(resource, "problem uploading extractor metadata...")
self.end_message(resource)
def process_message(self, connector, host, secret_key, resource,
parameters):
self.start_message(resource)
# Get left/right files and metadata
img_left, img_right, metadata = None, None, None
for fname in resource['local_paths']:
if fname.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(fname)
metadata = get_terraref_metadata(all_dsmd, 'stereoTop')
elif fname.endswith('_left.bin'):
img_left = fname
elif fname.endswith('_right.bin'):
img_right = fname
if None in [img_left, img_right, metadata]:
self.log_error(
"could not locate each of left+right+metadata in processing")
raise ValueError(
"could not locate each of left+right+metadata in processing")
# Determine output location & filenames
timestamp = resource['dataset_info']['name'].split(" - ")[1]
left_tiff = self.sensors.create_sensor_path(timestamp, opts=['left'])
right_tiff = self.sensors.create_sensor_path(timestamp, opts=['right'])
uploaded_file_ids = []
self.log_info(resource, "determining image shapes & gps bounds")
left_shape = bin2tiff.get_image_shape(metadata, 'left')
right_shape = bin2tiff.get_image_shape(metadata, 'right')
left_gps_bounds = geojson_to_tuples(
metadata['spatial_metadata']['left']['bounding_box'])
right_gps_bounds = geojson_to_tuples(
metadata['spatial_metadata']['right']['bounding_box'])
out_tmp_tiff = os.path.join(tempfile.gettempdir(),
resource['id'].encode('utf8'))
target_dsid = build_dataset_hierarchy(
host,
secret_key,
self.clowder_user,
self.clowder_pass,
self.clowderspace,
self.sensors.get_display_name(),
timestamp[:4],
timestamp[5:7],
timestamp[8:10],
leaf_ds_name=self.sensors.get_display_name() + ' - ' + timestamp)
if (not os.path.isfile(left_tiff)) or self.overwrite:
self.log_info(resource, "creating & uploading %s" % left_tiff)
left_image = bin2tiff.process_image(left_shape, img_left, None)
# Rename output.tif after creation to avoid long path errors
create_geotiff(left_image, left_gps_bounds, out_tmp_tiff, None,
False, self.extractor_info, metadata)
# TODO: we're moving zero byte files
shutil.move(out_tmp_tiff, left_tiff)
if left_tiff not in resource['local_paths']:
fileid = upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, target_dsid,
left_tiff)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
else:
self.log_info(
resource,
"file found in dataset already; not re-uploading")
self.created += 1
self.bytes += os.path.getsize(left_tiff)
if (not os.path.isfile(right_tiff)) or self.overwrite:
self.log_info(resource, "creating & uploading %s" % right_tiff)
right_image = bin2tiff.process_image(right_shape, img_right, None)
create_geotiff(right_image, right_gps_bounds, out_tmp_tiff, None,
False, self.extractor_info, metadata)
shutil.move(out_tmp_tiff, right_tiff)
if right_tiff not in resource['local_paths']:
fileid = upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, target_dsid,
right_tiff)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
else:
self.log_info(
resource,
"file found in dataset already; not re-uploading")
self.created += 1
self.bytes += os.path.getsize(right_tiff)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
ext_meta = build_metadata(host, self.extractor_info, resource['id'],
{"files_created": uploaded_file_ids},
'dataset')
self.log_info(resource, "uploading extractor metadata")
upload_metadata(connector, host, secret_key, resource['id'], ext_meta)
# Upload original Lemnatec metadata to new Level_1 dataset
md = get_terraref_metadata(all_dsmd)
md['raw_data_source'] = host + ("" if host.endswith("/") else
"/") + "datasets/" + resource['id']
lemna_md = build_metadata(host, self.extractor_info, target_dsid, md,
'dataset')
self.log_info(resource, "uploading LemnaTec metadata")
upload_metadata(connector, host, secret_key, target_dsid, lemna_md)
self.end_message(resource)
def process_message(self, connector, host, secret_key, resource, parameters):
self.start_message(resource)
# Get bin files and metadata
metadata = None
for f in resource['local_paths']:
# First check metadata attached to dataset in Clowder for item of interest
if f.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(f)
metadata = get_terraref_metadata(all_dsmd, "ps2Top")
# Otherwise, check if metadata was uploaded as a .json file
elif f.endswith('_metadata.json') and f.find('/_metadata.json') == -1 and metadata is None:
metadata = load_json_file(f)
frames = {}
for ind in range(0, 101):
format_ind = "{0:0>4}".format(ind) # e.g. 1 becomes 0001
for f in resource['local_paths']:
if f.endswith(format_ind+'.bin'):
frames[ind] = f
if None in [metadata] or len(frames) < 101:
self.log_error(resource, 'could not find all of frames/metadata')
return
# Determine output directory
timestamp = resource['dataset_info']['name'].split(" - ")[1]
hist_path = self.sensors.create_sensor_path(timestamp, opts=['combined_hist'])
coloredImg_path = self.sensors.create_sensor_path(timestamp, opts=['combined_pseudocolored'])
uploaded_file_ids = []
target_dsid = build_dataset_hierarchy(host, secret_key, self.clowder_user, self.clowder_pass, self.clowderspace,
self.sensors.get_display_name(),
timestamp[:4], timestamp[5:7], timestamp[8:10],
leaf_ds_name=self.sensors.get_display_name()+' - '+timestamp)
(img_width, img_height) = self.get_image_dimensions(metadata)
gps_bounds = geojson_to_tuples(metadata['spatial_metadata']['ps2Top']['bounding_box'])
self.log_info(resource, "image dimensions (w, h): (%s, %s)" % (img_width, img_height))
png_frames = {}
# skip 0101.bin since 101 is an XML file that lists the frame times
for ind in range(0, 101):
format_ind = "{0:0>4}".format(ind) # e.g. 1 becomes 0001
png_path = self.sensors.create_sensor_path(timestamp, opts=[format_ind])
tif_path = png_path.replace(".png", ".tif")
png_frames[ind] = png_path
if not os.path.exists(png_path) or self.overwrite:
self.log_info(resource, "generating and uploading %s" % png_path)
pixels = np.fromfile(frames[ind], np.dtype('uint8')).reshape([int(img_height), int(img_width)])
create_image(pixels, png_path)
create_geotiff(pixels, gps_bounds, tif_path, None, False, self.extractor_info, metadata)
if png_path not in resource['local_paths']:
fileid = upload_to_dataset(connector, host, secret_key, target_dsid, png_path)
uploaded_file_ids.append(fileid)
self.created += 1
self.bytes += os.path.getsize(png_path)
# Generate aggregate outputs
self.log_info(resource, "generating aggregates")
if not (os.path.exists(hist_path) and os.path.exists(coloredImg_path)) or self.overwrite:
# TODO: Coerce histogram and pseudocolor to geotiff?
self.analyze(int(img_width), int(img_height), png_frames, hist_path, coloredImg_path)
self.created += 2
self.bytes += os.path.getsize(hist_path) + os.path.getsize(coloredImg_path)
if hist_path not in resource['local_paths']:
fileid = upload_to_dataset(connector, host, secret_key, target_dsid, hist_path)
uploaded_file_ids.append(fileid)
if coloredImg_path not in resource['local_paths']:
fileid = upload_to_dataset(connector, host, secret_key, target_dsid, coloredImg_path)
uploaded_file_ids.append(fileid)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
metadata = build_metadata(host, self.extractor_info, target_dsid, {
"files_created": uploaded_file_ids}, 'dataset')
self.log_info(resource, "uploading extractor metadata")
upload_metadata(connector, host, secret_key, resource['id'], metadata)
self.end_message(resource)
metadata = utils.get_clowder_metadata(key, timestamp)
img_left = args.input + "/" + id + "_left.bin"
if not os.path.exists(img_left):
logger.error("Left image %s not found" % img_left)
sys.exit(1)
img_right = args.input + "/" + id + "_right.bin"
if not os.path.exists(img_right):
logger.error("Left image %s not found" % img_right)
sys.exit(1)
logger.debug("Processing raw image data")
left_shape = bin2tiff.get_image_shape(metadata, 'left')
right_shape = bin2tiff.get_image_shape(metadata, 'right')
left_gps_bounds = geojson_to_tuples(
metadata['spatial_metadata']['left']['bounding_box'])
right_gps_bounds = geojson_to_tuples(
metadata['spatial_metadata']['right']['bounding_box'])
left_image = bin2tiff.process_image(left_shape, img_left, None)
right_image = bin2tiff.process_image(right_shape, img_right, None)
logger.debug("Creating output directories")
sensors = Sensors(base=args.output, station="ua-mac", sensor="rgb_geotiff")
left_tiff = sensors.create_sensor_path(timestamp, opts=['left'])
right_tiff = sensors.create_sensor_path(timestamp, opts=['right'])
logger.debug("Generating geotiffs")
# TODO: Extractor Info is None here, which isn't good
create_geotiff(left_image, left_gps_bounds, left_tiff, None, False, None,
metadata)
create_geotiff(right_image, right_gps_bounds, right_tiff, None, False, None,
def process_message(self, connector, host, secret_key, resource, parameters):
self.start_message(resource)
# Get BIN file and metadata
bin_file, terra_md_full = None, None
for f in resource['local_paths']:
if f.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(f)
terra_md_full = get_terraref_metadata(all_dsmd, 'flirIrCamera')
elif f.endswith('_ir.bin'):
bin_file = f
if None in [bin_file, terra_md_full]:
raise ValueError("could not locate all files & metadata in processing")
timestamp = resource['dataset_info']['name'].split(" - ")[1]
# Fetch experiment name from terra metadata
season_name, experiment_name, updated_experiment = get_season_and_experiment(timestamp, 'flirIrCamera', terra_md_full)
if None in [season_name, experiment_name]:
raise ValueError("season and experiment could not be determined")
# Determine output directory
self.log_info(resource, "Hierarchy: %s / %s / %s / %s / %s / %s / %s" % (season_name, experiment_name, self.sensors.get_display_name(),
timestamp[:4], timestamp[5:7], timestamp[8:10], timestamp))
target_dsid = build_dataset_hierarchy_crawl(host, secret_key, self.clowder_user, self.clowder_pass, self.clowderspace,
season_name, experiment_name, self.sensors.get_display_name(),
timestamp[:4], timestamp[5:7], timestamp[8:10],
leaf_ds_name=self.sensors.get_display_name()+' - '+timestamp)
tiff_path = self.sensors.create_sensor_path(timestamp)
png_path = tiff_path.replace(".tif", ".png")
uploaded_file_ids = []
# Attach LemnaTec source metadata to Level_1 product
self.log_info(resource, "uploading LemnaTec metadata to ds [%s]" % target_dsid)
remove_metadata(connector, host, secret_key, target_dsid, self.extractor_info['name'])
terra_md_trim = get_terraref_metadata(all_dsmd)
if updated_experiment is not None:
terra_md_trim['experiment_metadata'] = updated_experiment
terra_md_trim['raw_data_source'] = host + ("" if host.endswith("/") else "/") + "datasets/" + resource['id']
level1_md = build_metadata(host, self.extractor_info, target_dsid, terra_md_trim, 'dataset')
upload_metadata(connector, host, secret_key, target_dsid, level1_md)
skipped_png = False
if not file_exists(png_path) or self.overwrite:
# Perform actual processing
self.log_info(resource, "creating & uploading %s" % png_path)
raw_data = numpy.fromfile(bin_file, numpy.dtype('<u2')).reshape([480, 640]).astype('float')
raw_data = numpy.rot90(raw_data, 3)
create_image(raw_data, png_path, self.scale_values)
self.created += 1
self.bytes += os.path.getsize(png_path)
else:
skipped_png = True
# Only upload the newly generated file to Clowder if it isn't already in dataset
found_in_dest = check_file_in_dataset(connector, host, secret_key, target_dsid, png_path, remove=self.overwrite)
if not found_in_dest or self.overwrite:
fileid = upload_to_dataset(connector, host, secret_key, target_dsid, png_path)
uploaded_file_ids.append(host + ("" if host.endswith("/") else "/") + "files/" + fileid)
if not file_exists(tiff_path) or self.overwrite:
# Generate temperature matrix and perform actual processing
self.log_info(resource, "creating & uploading %s" % tiff_path)
gps_bounds = geojson_to_tuples(terra_md_full['spatial_metadata']['flirIrCamera']['bounding_box'])
if skipped_png:
raw_data = numpy.fromfile(bin_file, numpy.dtype('<u2')).reshape([480, 640]).astype('float')
raw_data = numpy.rot90(raw_data, 3)
tc = getFlir.rawData_to_temperature(raw_data, terra_md_full) # get temperature
create_geotiff(tc, gps_bounds, tiff_path, None, True, self.extractor_info, terra_md_full)
self.created += 1
self.bytes += os.path.getsize(tiff_path)
# Only upload the newly generated file to Clowder if it isn't already in dataset
found_in_dest = check_file_in_dataset(connector, host, secret_key, target_dsid, tiff_path, remove=self.overwrite)
if not found_in_dest or self.overwrite:
fileid = upload_to_dataset(connector, host, secret_key, target_dsid, tiff_path)
uploaded_file_ids.append(host + ("" if host.endswith("/") else "/") + "files/" + fileid)
# Trigger additional extractors
self.log_info(resource, "triggering downstream extractors")
submit_extraction(connector, host, secret_key, target_dsid, "terra.plotclipper_tif")
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
if len(uploaded_file_ids) > 0:
extractor_md = build_metadata(host, self.extractor_info, target_dsid, {
"files_created": uploaded_file_ids
}, 'dataset')
self.log_info(resource, "uploading extractor metadata to raw dataset")
remove_metadata(connector, host, secret_key, resource['id'], self.extractor_info['name'])
upload_metadata(connector, host, secret_key, resource['id'], extractor_md)
self.end_message(resource)
def process_message(self, connector, host, secret_key, resource,
parameters):
self.start_message(resource)
# Get left/right files and metadata
img_left, img_right, metadata = None, None, None
for fname in resource['local_paths']:
if fname.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(fname)
terra_md_full = get_terraref_metadata(all_dsmd, 'stereoTop')
elif fname.endswith('_left.tif'):
img_left = fname
elif fname.endswith('_right.tif'):
img_right = fname
if None in [img_left, img_right, terra_md_full]:
raise ValueError(
"could not locate all files & metadata in processing")
timestamp = resource['dataset_info']['name'].split(" - ")[1]
target_dsid = resource['id']
left_rgb_mask_tiff = self.sensors.create_sensor_path(timestamp,
opts=['left'])
right_rgb_mask_tiff = self.sensors.create_sensor_path(timestamp,
opts=['right'])
uploaded_file_ids = []
right_ratio, left_ratio = 0, 0
left_bounds = geojson_to_tuples(
terra_md_full['spatial_metadata']['left']['bounding_box'])
right_bounds = geojson_to_tuples(
terra_md_full['spatial_metadata']['right']['bounding_box'])
#qual_md = get_extractor_metadata(all_dsmd, "terra.stereo-rgb.nrmac")
if (not file_exists(left_rgb_mask_tiff)) or self.overwrite:
self.log_info(resource, "creating %s" % left_rgb_mask_tiff)
#if qual_md and 'left_quality_score' in qual_md:
#left_ratio, left_rgb = gen_cc_enhanced(img_left, quality_score=int(qual_md['left_quality_score']))
left_ratio, left_rgb = gen_cc_enhanced(img_left)
if left_ratio is not None and left_rgb is not None:
# Bands must be reordered to avoid swapping R and B
left_rgb = cv2.cvtColor(left_rgb, cv2.COLOR_BGR2RGB)
create_geotiff(left_rgb, left_bounds, left_rgb_mask_tiff, None,
False, self.extractor_info, terra_md_full)
compress_geotiff(left_rgb_mask_tiff)
self.created += 1
self.bytes += os.path.getsize(left_rgb_mask_tiff)
else:
# If the masked version was not generated, delete any old version as well
self.log_info(
resource, "a faulty version exists; deleting %s" %
left_rgb_mask_tiff)
os.remove(left_rgb_mask_tiff)
found_in_dest = check_file_in_dataset(connector, host, secret_key,
target_dsid, left_rgb_mask_tiff)
if not found_in_dest:
self.log_info(resource, "uploading %s" % left_rgb_mask_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, target_dsid,
left_rgb_mask_tiff)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
if not self.leftonly:
if (not file_exists(right_rgb_mask_tiff)) or self.overwrite:
right_ratio, right_rgb = gen_cc_enhanced(img_right)
if right_ratio is not None and right_rgb is not None:
# Bands must be reordered to avoid swapping R and B
right_rgb = cv2.cvtColor(right_rgb, cv2.COLOR_BGR2RGB)
create_geotiff(right_rgb, right_bounds,
right_rgb_mask_tiff, None, False,
self.extractor_info, terra_md_full)
compress_geotiff(right_rgb_mask_tiff)
self.created += 1
self.bytes += os.path.getsize(right_rgb_mask_tiff)
else:
# If the masked version was not generated, delete any old version as well
self.log_info(
resource, "a faulty version exists; deleting %s" %
right_rgb_mask_tiff)
os.remove(right_rgb_mask_tiff)
found_in_dest = check_file_in_dataset(connector, host, secret_key,
target_dsid,
right_rgb_mask_tiff)
if not found_in_dest:
self.log_info(resource, "uploading %s" % right_rgb_mask_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, target_dsid,
right_rgb_mask_tiff)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
if len(uploaded_file_ids) > 0:
md = {
"files_created": uploaded_file_ids,
"left_mask_ratio": left_ratio
}
if not self.leftonly:
md["right_mask_ratio"] = right_ratio
extractor_md = build_metadata(host, self.extractor_info,
target_dsid, md, 'dataset')
self.log_info(resource,
"uploading extractor metadata to Lv1 dataset")
remove_metadata(connector, host, secret_key, resource['id'],
self.extractor_info['name'])
upload_metadata(connector, host, secret_key, resource['id'],
extractor_md)
self.end_message(resource)
def perform_process(transformer: transformer_class.Transformer, check_md: dict,
transformer_md: list, full_md: list) -> dict:
"""Performs the processing of the data
Arguments:
transformer: instance of transformer class
Return:
Returns a dictionary with the results of processing
"""
# pylint: disable=unused-argument
file_md = []
start_timestamp = datetime.datetime.utcnow()
file_list = __internal__.get_file_list(check_md['list_files']())
files_count = len(file_list)
# Find the metadata we're interested in for calibration parameters
terra_md = __internal__.find_terra_md(full_md)
if not terra_md:
raise RuntimeError("Unable to find TERRA REF specific metadata")
transformer_md = transformer.generate_transformer_md()
def generate_file_md(file_path: str) -> dict:
"""Returns file metadata for a file
Arguments:
file_path: the file to generate metadata for
Return:
Returns the metadata
"""
return {
'path': file_path,
'key': configuration.TRANSFORMER_SENSOR,
'metadata': {
'data': transformer_md
}
}
# Generate a list of approved file name endings
file_endings = ["{0:0>4}.bin".format(i) for i in range(0, 102)]
files_processed = 0
try:
img_width, img_height = __internal__.get_image_dimensions(terra_md)
gps_bounds = geojson_to_tuples(
terra_md['spatial_metadata']['ps2Top']['bounding_box'])
logging.debug("Image width and height: %s %s", str(img_width),
str(img_height))
logging.debug("Image geo bounds: %s", str(gps_bounds))
png_frames = {}
for one_file in file_list:
if one_file[-8:] in file_endings:
files_processed += 1
logging.debug("Processing file: '%s'", one_file)
try:
pixels = np.fromfile(one_file, np.dtype('uint8')).reshape(
[int(img_height), int(img_width)])
except ValueError:
logging.info(
"Ignoring ValueError exception while loading file '%s'",
one_file)
continue
png_filename = os.path.join(
check_md['working_folder'],
os.path.basename(one_file.replace('.bin', '.png')))
logging.info("Creating: '%s'", png_filename)
create_image(pixels, png_filename)
file_md.append(generate_file_md(png_filename))
png_frames[int(one_file[-8:-4])] = png_filename
tif_filename = os.path.join(
check_md['working_folder'],
os.path.basename(one_file.replace('.bin', '.tif')))
logging.info("Creating: '%s'", tif_filename)
create_geotiff(pixels, gps_bounds, tif_filename, None, False,
transformer_md, terra_md)
file_md.append(generate_file_md(tif_filename))
else:
logging.info("Skipping non-sensor file '%s'", one_file)
if files_processed > 0:
logging.info("Generating aggregates")
hist_path = os.path.join(check_md['working_folder'],
'combined_hist.png')
false_color_path = os.path.join(check_md['working_folder'],
'combined_pseudocolored.png')
__internal__.analyze(png_frames, hist_path, false_color_path)
file_md.append(generate_file_md(hist_path))
file_md.append(generate_file_md(false_color_path))
else:
logging.warning("No files were processed")
result = {
'code': 0,
'file': file_md,
configuration.TRANSFORMER_NAME: {
'version': configuration.TRANSFORMER_VERSION,
'utc_timestamp': datetime.datetime.utcnow().isoformat(),
'processing_time':
str(datetime.datetime.now() - start_timestamp),
'num_files_received': str(files_count),
'files_processed': str(files_processed)
}
}
except Exception as ex:
msg = 'Exception caught converting PSII files'
logging.exception(msg)
result = {'code': -1000, 'error': msg + ': ' + str(ex)}
return result
def process_message(self, connector, host, secret_key, resource,
parameters):
self.start_message(resource)
# Get left/right files and metadata
img_left, img_right, metadata = None, None, None
for fname in resource['local_paths']:
if fname.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(fname)
terra_md_full = get_terraref_metadata(all_dsmd, 'stereoTop')
elif fname.endswith('_left.tif'):
img_left = fname
elif fname.endswith('_right.tif'):
img_right = fname
if None in [img_left, img_right, terra_md_full]:
raise ValueError(
"could not locate all files & metadata in processing")
timestamp = resource['dataset_info']['name'].split(" - ")[1]
target_dsid = resource['id']
left_rgb_enh_tiff = self.sensors.create_sensor_path(timestamp,
opts=['left'])
right_rgb_enh_tiff = self.sensors.create_sensor_path(timestamp,
opts=['right'])
uploaded_file_ids = []
left_bounds = geojson_to_tuples(
terra_md_full['spatial_metadata']['left']['bounding_box'])
right_bounds = geojson_to_tuples(
terra_md_full['spatial_metadata']['right']['bounding_box'])
if not file_exists(left_rgb_enh_tiff) or self.overwrite:
self.log_info(resource, "creating %s" % left_rgb_enh_tiff)
EI = getEnhancedImage(img_left)
create_geotiff(EI, left_bounds, left_rgb_enh_tiff)
self.created += 1
self.bytes += os.path.getsize(left_rgb_enh_tiff)
found_in_dest = check_file_in_dataset(connector,
host,
secret_key,
target_dsid,
left_rgb_enh_tiff,
remove=self.overwrite)
if not found_in_dest:
self.log_info(resource, "uploading %s" % left_rgb_enh_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, target_dsid,
left_rgb_enh_tiff)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
if not file_exists(right_rgb_enh_tiff) or self.overwrite:
self.log_info(resource, "creating %s" % right_rgb_enh_tiff)
EI = getEnhancedImage(img_right)
create_geotiff(EI, right_bounds, right_rgb_enh_tiff)
self.created += 1
self.bytes += os.path.getsize(right_rgb_enh_tiff)
found_in_dest = check_file_in_dataset(connector,
host,
secret_key,
target_dsid,
right_rgb_enh_tiff,
remove=self.overwrite)
if not found_in_dest:
self.log_info(resource, "uploading %s" % right_rgb_enh_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user,
self.clowder_pass, target_dsid,
right_rgb_enh_tiff)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
ext_meta = build_metadata(host, self.extractor_info, target_dsid,
{"files_created": uploaded_file_ids},
'dataset')
self.log_info(resource, "uploading extractor metadata")
remove_metadata(connector, host, secret_key, target_dsid,
self.extractor_info['name'])
upload_metadata(connector, host, secret_key, target_dsid, ext_meta)
self.end_message(resource)
def process_message(self, connector, host, secret_key, resource,
parameters):
self.start_message()
# Get BIN file and metadata
bin_file, metadata = None, None
for f in resource['local_paths']:
# First check metadata attached to dataset in Clowder for item of interest
if f.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(f)
metadata = get_terraref_metadata(all_dsmd, 'flirIrCamera')
# Otherwise, check if metadata was uploaded as a .json file
elif f.endswith('_ir.bin'):
bin_file = f
if None in [bin_file, metadata]:
logging.getLogger(__name__).error(
'could not find all both of ir.bin/metadata')
return
# Determine output directory
timestamp = resource['dataset_info']['name'].split(" - ")[1]
png_path = self.sensors.create_sensor_path(timestamp, ext='png')
tiff_path = self.sensors.create_sensor_path(timestamp)
uploaded_file_ids = []
target_dsid = build_dataset_hierarchy(
host,
secret_key,
self.clowder_user,
self.clowder_pass,
self.clowderspace,
self.sensors.get_display_name(),
timestamp[:4],
timestamp[5:7],
timestamp[8:10],
leaf_ds_name=self.sensors.get_display_name() + ' - ' + timestamp)
skipped_png = False
if not os.path.exists(png_path) or self.overwrite:
logging.getLogger(__name__).info("Generating %s" % png_path)
# get raw data from bin file
raw_data = numpy.fromfile(bin_file, numpy.dtype('<u2')).reshape(
[480, 640]).astype('float')
raw_data = numpy.rot90(raw_data, 3)
create_image(raw_data, png_path, self.scale_values)
# Only upload the newly generated file to Clowder if it isn't already in dataset
if png_path not in resource["local_paths"]:
fileid = upload_to_dataset(connector, host, secret_key,
target_dsid, png_path)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
self.created += 1
self.bytes += os.path.getsize(png_path)
else:
skipped_png = True
if not os.path.exists(tiff_path) or self.overwrite:
logging.getLogger(__name__).info("Generating temperature matrix")
gps_bounds = geojson_to_tuples(
metadata['spatial_metadata']['flirIrCamera']['bounding_box'])
if skipped_png:
raw_data = numpy.fromfile(bin_file,
numpy.dtype('<u2')).reshape(
[480, 640]).astype('float')
raw_data = numpy.rot90(raw_data, 3)
tc = getFlir.rawData_to_temperature(raw_data,
metadata) # get temperature
logging.getLogger(__name__).info("Creating %s" % tiff_path)
# Rename temporary tif after creation to avoid long path errors
out_tmp_tiff = os.path.join(tempfile.gettempdir(),
resource['id'].encode('utf8'))
create_geotiff(tc, gps_bounds, out_tmp_tiff, None, True,
self.extractor_info, metadata)
shutil.move(out_tmp_tiff, tiff_path)
if tiff_path not in resource["local_paths"]:
fileid = upload_to_dataset(connector, host, secret_key,
target_dsid, tiff_path)
uploaded_file_ids.append(host +
("" if host.endswith("/") else "/") +
"files/" + fileid)
self.created += 1
self.bytes += os.path.getsize(tiff_path)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
metadata = build_metadata(host, self.extractor_info, target_dsid,
{"files_created": uploaded_file_ids},
'dataset')
upload_metadata(connector, host, secret_key, resource['id'], metadata)
# Upload original Lemnatec metadata to new Level_1 dataset
md = get_terraref_metadata(all_dsmd)
md['raw_data_source'] = host + ("" if host.endswith("/") else
"/") + "datasets/" + resource['id']
lemna_md = build_metadata(host, self.extractor_info, target_dsid, md,
'dataset')
upload_metadata(connector, host, secret_key, target_dsid, lemna_md)
self.end_message()
def process_message(self, connector, host, secret_key, resource, parameters):
self.start_message(resource)
# Get left/right files and metadata
img_left, img_right, metadata = None, None, None
for fname in resource['local_paths']:
if fname.endswith('_dataset_metadata.json'):
all_dsmd = load_json_file(fname)
terra_md_full = get_terraref_metadata(all_dsmd, 'stereoTop')
elif fname.endswith('_left.tif'):
img_left = fname
elif fname.endswith('_right.tif'):
img_right = fname
if None in [img_left, img_right, terra_md_full]:
raise ValueError("could not locate all files & metadata in processing")
timestamp = resource['dataset_info']['name'].split(" - ")[1]
target_dsid = resource['id']
left_nrmac_tiff = self.sensors.create_sensor_path(timestamp, opts=['left'])
right_nrmac_tiff = self.sensors.create_sensor_path(timestamp, opts=['right'])
uploaded_file_ids = []
self.log_info(resource, "determining image quality")
left_qual = getImageQuality(img_left)
if not self.leftonly:
right_qual = getImageQuality(img_right)
left_bounds = geojson_to_tuples(terra_md_full['spatial_metadata']['left']['bounding_box'])
right_bounds = geojson_to_tuples(terra_md_full['spatial_metadata']['right']['bounding_box'])
if not file_exists(left_nrmac_tiff) or self.overwrite:
self.log_info(resource, "creating %s" % left_nrmac_tiff)
create_geotiff(np.array([[left_qual, left_qual],[left_qual, left_qual]]), left_bounds,
left_nrmac_tiff, None, True, self.extractor_info, terra_md_full, compress=True)
self.created += 1
self.bytes += os.path.getsize(left_nrmac_tiff)
found_in_dest = check_file_in_dataset(connector, host, secret_key, target_dsid, left_nrmac_tiff,
remove=self.overwrite)
if not found_in_dest or self.overwrite:
self.log_info(resource, "uploading %s" % left_nrmac_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user, self.clowder_pass, target_dsid,
left_nrmac_tiff)
uploaded_file_ids.append(host + ("" if host.endswith("/") else "/") + "files/" + fileid)
if not self.leftonly:
if (not file_exists(right_nrmac_tiff) or self.overwrite):
self.log_info(resource, "creating %s" % right_nrmac_tiff)
create_geotiff(np.array([[right_qual, right_qual],[right_qual, right_qual]]), right_bounds,
right_nrmac_tiff, None, True, self.extractor_info, terra_md_full, compress=True)
self.created += 1
self.bytes += os.path.getsize(right_nrmac_tiff)
found_in_dest = check_file_in_dataset(connector, host, secret_key, target_dsid, right_nrmac_tiff,
remove=self.overwrite)
if not found_in_dest or self.overwrite:
self.log_info(resource, "uploading %s" % right_nrmac_tiff)
fileid = upload_to_dataset(connector, host, self.clowder_user, self.clowder_pass, target_dsid,
right_nrmac_tiff)
uploaded_file_ids.append(host + ("" if host.endswith("/") else "/") + "files/" + fileid)
# Tell Clowder this is completed so subsequent file updates don't daisy-chain
md = {
"files_created": uploaded_file_ids,
"left_quality_score": left_qual
}
if not self.leftonly:
md["right_quality_score"] = right_qual
extractor_md = build_metadata(host, self.extractor_info, resource['id'], md, 'file')
self.log_info(resource, "uploading extractor metadata to Lv1 dataset")
remove_metadata(connector, host, secret_key, resource['id'], self.extractor_info['name'])
upload_metadata(connector, host, secret_key, resource['id'], extractor_md)
self.end_message(resource)