From 4b238a25903d8abf9fb0b94a42094c9bb700e648 Mon Sep 17 00:00:00 2001
From: Tiago Freitas Pereira <tiagofrepereira@gmail.com>
Date: Fri, 19 Jun 2020 09:08:41 +0200
Subject: [PATCH] Comparison app
---
bob/bio/base/script/compare_samples.py | 100 ++++++++++++++++++
bob/bio/base/script/vanilla_biometrics.py | 33 ++++--
.../base/script/vanilla_biometrics_ztnorm.py | 14 +--
setup.py | 1 +
4 files changed, 129 insertions(+), 19 deletions(-)
create mode 100644 bob/bio/base/script/compare_samples.py
diff --git a/bob/bio/base/script/compare_samples.py b/bob/bio/base/script/compare_samples.py
new file mode 100644
index 00000000..bab5de05
--- /dev/null
+++ b/bob/bio/base/script/compare_samples.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
+
+
+"""Executes biometric pipeline"""
+
+import click
+
+from bob.extension.scripts.click_helper import (
+ verbosity_option,
+ ResourceOption,
+ ConfigCommand,
+)
+import bob.io.base
+import bob.io.image
+
+import logging
+import os
+import itertools
+import dask.bag
+
+# from bob.bio.base.pipelines.vanilla_biometrics import (
+# VanillaBiometricsPipeline,
+# BioAlgorithmCheckpointWrapper,
+# BioAlgorithmDaskWrapper,
+# checkpoint_vanilla_biometrics,
+# dask_vanilla_biometrics,
+# dask_get_partition_size,
+# FourColumnsScoreWriter,
+# CSVScoreWriter,
+# )
+# from dask.delayed import Delayed
+# import pkg_resources
+from bob.extension.config import load as chain_load
+from bob.pipelines.utils import isinstance_nested
+from bob.bio.base.utils import get_resource_filename
+from .vanilla_biometrics import compute_scores, load_database_pipeline
+from bob.pipelines import Sample, SampleSet
+
+
+logger = logging.getLogger(__name__)
+
+
+EPILOG = """\b
+
+
+ Command line examples\n
+ -----------------------
+
+
+"""
+
+
+@click.command(epilog=EPILOG)
+@click.argument("samples", nargs=-1)
+@click.option(
+ "--pipeline",
+ "-p",
+ required=True,
+ cls=ResourceOption,
+ entry_point_group="bob.bio.pipeline",
+ help="Vanilla biometrics pipeline composed of a scikit-learn Pipeline and a BioAlgorithm",
+)
+@click.option(
+ "--dask-client",
+ "-l",
+ required=False,
+ cls=ResourceOption,
+ help="Dask client for the execution of the pipeline.",
+)
+@verbosity_option(cls=ResourceOption)
+def compare_samples(
+ samples, pipeline, dask_client, **kwargs,
+):
+ """Compare several samples all vs all using one vanilla biometrics pipeline
+
+ """
+
+ if len(samples) == 1:
+ raise ValueError(
+ "It's necessary to have at least two samples for the comparison"
+ )
+
+ sample_sets = [
+ SampleSet([Sample(bob.io.base.load(s), key=str(i))], key=str(i))
+ for i, s in enumerate(samples)
+ ]
+
+ import ipdb; ipdb.set_trace()
+ for e in sample_sets:
+ biometric_references = pipeline.create_biometric_reference([e])
+ scores = pipeline.compute_scores(biometric_references, sample_sets)
+ pass
+
+ # B = bob.io.base.load(p)
+ # pipeline.biometric_algorithm
+
+ if dask_client is not None:
+ dask_client.shutdown()
diff --git a/bob/bio/base/script/vanilla_biometrics.py b/bob/bio/base/script/vanilla_biometrics.py
index 74be6c84..88054034 100644
--- a/bob/bio/base/script/vanilla_biometrics.py
+++ b/bob/bio/base/script/vanilla_biometrics.py
@@ -74,16 +74,32 @@ def post_process_scores(pipeline, scores, path):
return pipeline.post_process(writed_scores, path)
+def load_database_pipeline(database, pipeline):
+ # It's necessary to chain load 2 resources together
+ pipeline_config = get_resource_filename(pipeline, "bob.bio.pipeline")
+
+ if database is None:
+ vanilla_pipeline = chain_load([pipeline_config])
+ if hasattr(vanilla_pipeline, "database"):
+ return vanilla_pipeline.database, vanilla_pipeline.pipeline
+ else:
+ raise ValueError("Database was not set. Please look in `bob bio pipelines vanilla-biometrics --help` for more information")
+ else:
+ database_config = get_resource_filename(database, "bob.bio.database")
+ vanilla_pipeline = chain_load([database_config, pipeline_config])
+ return vanilla_pipeline.database, vanilla_pipeline.pipeline
+
+
@click.command(
entry_point_group="bob.bio.pipeline.config", cls=ConfigCommand, epilog=EPILOG,
)
@click.option(
- "--pipeline", "-p", required=True, help="Vanilla biometrics pipeline",
+ "--pipeline", "-p", required=True, help="Vanilla biometrics pipeline composed of a scikit-learn Pipeline and a BioAlgorithm",
)
@click.option(
"--database",
"-d",
- required=True,
+ required=False,
help="Biometric Database connector (class that implements the methods: `background_model_samples`, `references` and `probes`)",
)
@click.option(
@@ -185,15 +201,12 @@ def vanilla_biometrics(
if not os.path.exists(output):
os.makedirs(output, exist_ok=True)
- # It's necessary to chain load 2 resources together
- pipeline_config = get_resource_filename(pipeline, "bob.bio.pipeline")
- database_config = get_resource_filename(database, "bob.bio.database")
- vanilla_pipeline = chain_load([database_config, pipeline_config])
- dask_client = chain_load([dask_client]).dask_client
-
# Picking the resources
- database = vanilla_pipeline.database
- pipeline = vanilla_pipeline.pipeline
+ database, pipeline = load_database_pipeline(database, pipeline)
+
+ if dask_client is not None:
+ dask_client = chain_load([dask_client]).dask_client
+
if write_metadata_scores:
pipeline.score_writer = CSVScoreWriter(os.path.join(output, "./tmp"))
else:
diff --git a/bob/bio/base/script/vanilla_biometrics_ztnorm.py b/bob/bio/base/script/vanilla_biometrics_ztnorm.py
index 57f5bbb9..ce00590a 100644
--- a/bob/bio/base/script/vanilla_biometrics_ztnorm.py
+++ b/bob/bio/base/script/vanilla_biometrics_ztnorm.py
@@ -34,7 +34,7 @@ from dask.delayed import Delayed
from bob.bio.base.utils import get_resource_filename
from bob.extension.config import load as chain_load
from bob.pipelines.utils import isinstance_nested
-from .vanilla_biometrics import compute_scores, post_process_scores
+from .vanilla_biometrics import compute_scores, post_process_scores, load_database_pipeline
import copy
logger = logging.getLogger(__name__)
@@ -67,7 +67,7 @@ EPILOG = """\b
entry_point_group="bob.pipelines.config", cls=ConfigCommand, epilog=EPILOG,
)
@click.option(
- "--pipeline", "-p", required=True, help="An entry point or a configuration file containing a `VanillaBiometricsPipeline`.",
+ "--pipeline", "-p", required=True, help="Vanilla biometrics pipeline composed of a scikit-learn Pipeline and a BioAlgorithm",
)
@click.option(
"--database",
@@ -199,16 +199,12 @@ def vanilla_biometrics_ztnorm(
os.makedirs(output, exist_ok=True)
# It's necessary to chain load 2 resources together
- pipeline_config = get_resource_filename(pipeline, "bob.bio.pipeline")
- database_config = get_resource_filename(database, "bob.bio.database")
- vanilla_pipeline = chain_load([database_config, pipeline_config])
+ # Picking the resources
+ database, pipeline = load_database_pipeline(database, pipeline)
+
if dask_client is not None:
dask_client = chain_load([dask_client]).dask_client
- # Picking the resources
- database = vanilla_pipeline.database
- pipeline = vanilla_pipeline.pipeline
-
if write_metadata_scores:
pipeline.score_writer = CSVScoreWriter(os.path.join(output, "./tmp"))
else:
diff --git a/setup.py b/setup.py
index 57102217..70ff0ebe 100644
--- a/setup.py
+++ b/setup.py
@@ -133,6 +133,7 @@ setup(
'baseline = bob.bio.base.script.baseline:baseline',
'sort = bob.bio.base.script.sort:sort',
'pipelines = bob.bio.base.script.pipelines:pipelines',
+ 'compare-samples = bob.bio.base.script.compare_samples:compare_samples',
],
# annotators
--
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