Fix --metrics-file argument.

config/default_dataset_metrics.py

@@ -2,8 +2,6 @@
 # Import these modules to ensure the metrics are registered
 import lsst.ap.association.metrics  # noqa: F401
 
-config.jobFileTemplate = "ap_verify.metricTask{id}.{dataId}.verify.json"
-
 ppdbConfigs = ["totalUnassociatedDiaObjects"]
 config.measurers = ppdbConfigs
 

config/default_image_metrics.py

@@ -3,8 +3,6 @@
 import lsst.ip.diffim.metrics  # noqa: F401
 import lsst.ap.association.metrics  # noqa: F401
 
-config.jobFileTemplate = "ap_verify.metricTask{id}.{dataId}.verify.json"
-
 metadataConfigs = ["numNewDiaObjects",
                    "numUnassociatedDiaObjects",
                    "fracUpdatedDiaObjects"]

python/lsst/ap/verify/ap_verify.py

@@ -30,17 +30,13 @@
 __all__ = ["runApVerify", "runIngestion"]
 
 import argparse
-import copy
-import os
 import re
 
 import lsst.log
-import lsst.utils
-from lsst.verify.gen2tasks import MetricsControllerTask
 
 from .dataset import Dataset
 from .ingestion import ingestDataset
-from .metrics import MetricsParser
+from .metrics import MetricsParser, computeMetrics
 from .pipeline_driver import ApPipeParser, runApPipe
 from .workspace import Workspace
 
@@ -59,12 +55,6 @@ def __init__(self):
                           required=True, help='The source of data to pass through the pipeline.')
         self.add_argument('--output', required=True,
                           help='The location of the workspace to use for pipeline repositories.')
-        self.add_argument('--dataset-metrics-config',
-                          help='The config file specifying the dataset-level metrics to measure. '
-                               'Defaults to config/default_dataset_metrics.py.')
-        self.add_argument('--image-metrics-config',
-                          help='The config file specifying the image-level metrics to measure. '
-                               'Defaults to config/default_image_metrics.py.')
 
 
 class _ApVerifyParser(argparse.ArgumentParser):
@@ -139,87 +129,6 @@ def __call__(self, _parser, namespace, values, _option_string=None):
         setattr(namespace, self.dest, Dataset(values))
 
 
-def _measureFinalProperties(workspace, dataIds, args):
-    """Measure any metrics that apply to the final result of the AP pipeline,
-    rather than to a particular processing stage.
-
-    Parameters
-    ----------
-    workspace : `lsst.ap.verify.workspace.Workspace`
-        The abstract location containing input and output repositories.
-    dataIds : `lsst.pipe.base.DataIdContainer`
-        The data IDs ap_pipe was run on. Each data ID must be complete.
-    args : `argparse.Namespace`
-        Command-line arguments, including arguments controlling output.
-    """
-    imageConfig = _getMetricsConfig(args.image_metrics_config, "default_image_metrics.py")
-    _runMetricTasks(imageConfig, dataIds.refList)
-
-    datasetConfig = _getMetricsConfig(args.dataset_metrics_config, "default_dataset_metrics.py")
-    _runMetricTasks(datasetConfig, [workspace.workButler.dataRef("apPipe_config")])
-
-
-def _getMetricsConfig(userFile, defaultFile):
-    """Load a metrics config based on program settings.
-
-    Parameters
-    ----------
-    userFile : `str` or `None`
-        The path provided by the user for this config file.
-    defaultFile : `str`
-        The filename (not a path) of the default config file.
-
-    Returns
-    -------
-    config : `lsst.verify.gen2tasks.MetricsControllerConfig`
-        The config from ``userFile`` if the user provided one, otherwise the
-        default config.
-    """
-    timingConfig = MetricsControllerTask.ConfigClass()
-
-    if userFile is not None:
-        timingConfig.load(userFile)
-    else:
-        timingConfig.load(os.path.join(lsst.utils.getPackageDir("ap_verify"), "config", defaultFile))
-    return timingConfig
-
-
-def _runMetricTasks(config, dataRefs):
-    """Run MetricControllerTask on a single dataset.
-
-    Parameters
-    ----------
-    config : `lsst.verify.gen2tasks.MetricsControllerConfig`
-        The config for running `~lsst.verify.gen2tasks.MetricsControllerTask`.
-    dataRefs : `list` [`lsst.daf.persistence.ButlerDataRef`]
-        The data references over which to compute metrics. The granularity
-        determines the metric granularity; see
-        `MetricsControllerTask.runDataRef` for more details.
-    """
-    allMetricTasks = MetricsControllerTask(config)
-    allMetricTasks.runDataRefs([_sanitizeRef(ref) for ref in dataRefs])
-
-
-def _sanitizeRef(dataRef):
-    """Remove data ID tags that can cause problems when loading arbitrary
-    dataset types.
-
-    Parameters
-    ----------
-    dataRef : `lsst.daf.persistence.ButlerDataRef`
-        The dataref to sanitize.
-
-    Returns
-    -------
-    clean : `lsst.daf.persistence.ButlerDataRef`
-        A dataref that is safe to use.
-    """
-    newDataRef = copy.deepcopy(dataRef)
-    if "hdu" in newDataRef.dataId:
-        del newDataRef.dataId["hdu"]
-    return newDataRef
-
-
 def runApVerify(cmdLine=None):
     """Execute the AP pipeline while handling metrics.
 
@@ -244,7 +153,7 @@ def runApVerify(cmdLine=None):
 
     log.info('Running pipeline...')
     expandedDataIds = runApPipe(workspace, args)
-    _measureFinalProperties(workspace, expandedDataIds, args)
+    computeMetrics(workspace, expandedDataIds, args)
 
 
 def runIngestion(cmdLine=None):

python/lsst/ap/verify/metrics.py

@@ -28,11 +28,16 @@
 ``ap_verify`` module or in the appropriate pipeline step, as appropriate.
 """
 
-__all__ = ["MetricsParser"]
+__all__ = ["MetricsParser", "computeMetrics"]
 
 import argparse
+import copy
+import os
 import warnings
 
+import lsst.utils
+from lsst.verify.gen2tasks import MetricsControllerTask
+
 
 class MetricsParser(argparse.ArgumentParser):
     """An argument parser for data needed by metrics activities.
@@ -54,6 +59,12 @@ def __init__(self):
                           action=DeprecatedAction,
                           deprecationReason="SQuaSH upload is no longer supported",
                           help='Do NOT submit metrics to SQuaSH.')
+        self.add_argument('--dataset-metrics-config',
+                          help='The config file specifying the dataset-level metrics to measure. '
+                               'Defaults to config/default_dataset_metrics.py.')
+        self.add_argument('--image-metrics-config',
+                          help='The config file specifying the image-level metrics to measure. '
+                               'Defaults to config/default_image_metrics.py.')
 
 
 class DeprecatedAction(argparse.Action):
@@ -78,3 +89,93 @@ def __call__(self, _parser, _namespace, _values, option_string=None):
         message = "%s has been deprecated, because %s. It will be removed in a future version." \
             % (option_string, self.reason)
         warnings.warn(message, category=FutureWarning)
+
+
+def computeMetrics(workspace, dataIds, args):
+    """Measure any metrics that apply to the final result of the AP pipeline,
+    rather than to a particular processing stage.
+
+    Parameters
+    ----------
+    workspace : `lsst.ap.verify.workspace.Workspace`
+        The abstract location containing input and output repositories.
+    dataIds : `lsst.pipe.base.DataIdContainer`
+        The data IDs ap_pipe was run on. Each data ID must be complete.
+    args : `argparse.Namespace`
+        Command-line arguments, including arguments controlling output.
+    """
+    imageConfig = _getMetricsConfig(args.image_metrics_config,
+                                    "default_image_metrics.py",
+                                    args.metrics_file)
+    _runMetricTasks(imageConfig, dataIds.refList)
+
+    datasetConfig = _getMetricsConfig(args.dataset_metrics_config,
+                                      "default_dataset_metrics.py",
+                                      args.metrics_file)
+    _runMetricTasks(datasetConfig, [workspace.workButler.dataRef("apPipe_config")])
+
+
+def _getMetricsConfig(userFile, defaultFile, metricsOutputTemplate=None):
+    """Load a metrics config based on program settings.
+
+    Parameters
+    ----------
+    userFile : `str` or `None`
+        The path provided by the user for this config file.
+    defaultFile : `str`
+        The filename (not a path) of the default config file.
+    metricsOutputTemplate : `str` or `None`
+        The files to which to write metrics. If not `None`, this argument
+        overrides any output files set by either config file.
+
+    Returns
+    -------
+    config : `lsst.verify.gen2tasks.MetricsControllerConfig`
+        The config from ``userFile`` if the user provided one, otherwise the
+        default config.
+    """
+    timingConfig = MetricsControllerTask.ConfigClass()
+
+    if userFile is not None:
+        timingConfig.load(userFile)
+    else:
+        timingConfig.load(os.path.join(lsst.utils.getPackageDir("ap_verify"), "config", defaultFile))
+    if metricsOutputTemplate:
+        timingConfig.jobFileTemplate = metricsOutputTemplate
+    return timingConfig
+
+
+def _runMetricTasks(config, dataRefs):
+    """Run MetricControllerTask on a single dataset.
+
+    Parameters
+    ----------
+    config : `lsst.verify.gen2tasks.MetricsControllerConfig`
+        The config for running `~lsst.verify.gen2tasks.MetricsControllerTask`.
+    dataRefs : `list` [`lsst.daf.persistence.ButlerDataRef`]
+        The data references over which to compute metrics. The granularity
+        determines the metric granularity; see
+        `MetricsControllerTask.runDataRef` for more details.
+    """
+    allMetricTasks = MetricsControllerTask(config)
+    allMetricTasks.runDataRefs([_sanitizeRef(ref) for ref in dataRefs])
+
+
+def _sanitizeRef(dataRef):
+    """Remove data ID tags that can cause problems when loading arbitrary
+    dataset types.
+
+    Parameters
+    ----------
+    dataRef : `lsst.daf.persistence.ButlerDataRef`
+        The dataref to sanitize.
+
+    Returns
+    -------
+    clean : `lsst.daf.persistence.ButlerDataRef`
+        A dataref that is safe to use.
+    """
+    newDataRef = copy.deepcopy(dataRef)
+    if "hdu" in newDataRef.dataId:
+        del newDataRef.dataId["hdu"]
+    return newDataRef