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Add --classify-batch-size arg #6

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Add --classify-batch-size arg #6

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18 changes: 16 additions & 2 deletions src/python/ifcb_analysis/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ def process_bin(
model_config: classify.KerasModelConfig,
extract_images: bool = True,
classify_images: bool = True,
classify_batch_size: int = None,
force: bool = False,
dask_log_path: str = None,
dask_log_level: int = None,
Expand Down Expand Up @@ -158,7 +159,7 @@ def process_bin(

if classify_images:
logging.info(f'Classifying images and saving to {class_fname}')
predictions_df = classify.predict(model_config, image_stack)
predictions_df = classify.predict(model_config, image_stack, classify_batch_size)

# Since classify.predict (which calls Model.predict) is run in a for loop, memory consumption
# will build up and result in an OOM error, so we excplicitly clear it out after each model run.
Expand Down Expand Up @@ -278,6 +279,7 @@ def process(
date_dirs: bool = True,
extract_images: bool = True,
classify_images: bool = True,
classify_batch_size: int = None,
force: bool = False,
use_dask: bool = True,
dask_log_path: str = None,
Expand Down Expand Up @@ -321,6 +323,7 @@ def process(
[model_config] * len(bins),
[extract_images] * len(bins),
[classify_images] * len(bins),
[classify_batch_size] * len(bins),
[force] * len(bins)
]

Expand Down Expand Up @@ -348,7 +351,15 @@ def process(
outdir = output_dir

try:
process_bin(bin, outdir, model_config, extract_images, classify_images, force)
process_bin(
file=bin,
outdir=outdir,
model_config=model_config,
extract_images=extract_images,
classify_images=classify_images,
classify_batch_size=classify_batch_size,
force=force,
)
except Exception as e:
logging.error(f'Error processing {bin}: {e}')

Expand All @@ -363,6 +374,7 @@ def yaml_config_callback(ctx, param, value):
@click.command()
@click.option('--extract-images/--no-extract-images', default=True)
@click.option('--classify-images/--no-classify-images', default=True)
@click.option('--classify-batch-size', type=click.INT, default=64)
@click.option('--force/--no-force', default=False)
@click.option('--log-level', default='INFO')
@click.option('--log-file', type=click.Path(writable=True, dir_okay=False))
Expand All @@ -386,6 +398,7 @@ def cli(
ctx,
extract_images: bool,
classify_images: bool,
classify_batch_size: int,
force: bool,
log_level: str,
log_file: Path,
Expand Down Expand Up @@ -439,6 +452,7 @@ def cli(
date_dirs=date_dirs,
extract_images=extract_images,
classify_images=classify_images,
classify_batch_size=classify_batch_size,
force=force,
use_dask=use_dask,
dask_log_path=dask_log_path,
Expand Down