Source code for asterism.analysis_pipelines.morphometric_features_extraction
"""
Overview
--------
This module provides the implementation of the :class:`.MorphometricFeatureExtractionPipeline` class,
used to create the pipeline for the morphometric features extraction.
The processes in the pipeline are orchestrated by the :func:`.do_morphometric_feature_extraction_pipeline_func`, according to
the algorithm shown by the following flow chart:
.. digraph:: deblending
subgraph morphometrt_flow {
"Image"->"do_src_detection" -> "cluster_list"->"do_morphometric_input_products"->"morph_input_prods"->"do_morphometric_features_extraction";
"Image" [shape=parallelogram]
"do_src_detection" [shape=polygon,sides=4]
"cluster_list" [shape=parallelogram]
"do_morphometric_input_products" [shape=polygon,sides=4]
"morph_input_prods" [shape=parallelogram]
"do_morphometric_features_extraction" [shape=polygon,sides=4]
}
Classes and Inheritance Structure
----------------------------------------------
.. inheritance-diagram:: asterism.analysis_pipelines.morphometric_features_extraction.MorphometricFeatureExtractionPipeline
Summary
---------
.. autosummary::
do_morphometric_feature_extraction_pipeline_func
MorphometricFeatureExtractionPipeline
Module API
-----------
"""
from __future__ import division, absolute_import, print_function
from ..pipeline_manager.analysis_pipeline import AnalysisPipeline
from ..analysis_processes.source_detection import DoSrcDetectionProcess
from ..analysis_processes.morphometric_features_input_products import DoMorphometricInputProducts
from ..analysis_processes.morphometric_feature_extraction import DoMorphometricFeaturesExtraction
from ..plotting.plot_tools import analysis_plot
from ..core.clustering.cluster_tools import get_cluster_closest_to_position
from ..core.image_manager.image import Image
__author__ = 'andrea tramacere'
[docs]def do_morphometric_feature_extraction_pipeline_func(pipeline,image,image_id=None,input_seg_map=None,**kwargs):
"""
Function implementing the Pipeline algorithm for the morphometric features extraction.
- do_src_detection :class:`.DoSrcDetectionProcess` , extraction of clusters list from input Image
- selection of central cluster from clusters list
- do_morphometric_input_products :class:`.DoMorphometricInputProducts`, extraction of :class:'asterism.analysis_processes.morphometric_features_input_products.MorphometryInputData'
- do_morphometric_features_extraction :class:`.DoMorphometricFeaturesExtraction`
Parameters
-----------
pipeline : :class:`.MorphometricFeatureExtractionPipeline`
instance of the base :class:`.AnalysisPipeline` class
image : :class:`.Image`
instance of the class used as input for different processes
image_id : int
id of the image
**kwargs:
Returns
-------
morphometric_features_analysis_products : :class:`asterism.pipeline_manager.analysis_products.AnalysisProcessProducts`
class instance storing the analysis products for this pipeline
"""
#Type checking for image
if isinstance(image,Image)==True:
pass
else:
raise TypeError('image is not instance of Image class')
#Detection Process
analysis_prod_collection=pipeline.do_src_detection.run(image,image_id=image_id,input_seg_map=input_seg_map)
cluster_list=analysis_prod_collection.get_product_by_name('cluster_list').prods
if cluster_list==[]:
#set failed
cluster_list=[None]
#bkg_lvl=analysis_prod_collection.get_product_by_name('bkg_threshold').prods
#x_c=image._center_x
#y_c=image._center_y
#The source at the center of the image is used
#central_cluster=get_cluster_closest_to_position(cluster_list,x_c=x_c,y_c=y_c)
#Products to be used as input for morphometric features extraction are build
for ID,cl in enumerate(cluster_list):
if cl is None:
cluster_th_level=None
x_c=None
y_c=None
cl_id=-1
else:
cluster_th_level=cl.flux.min()
x_c=cl.x_c
y_c=cl.y_c
cl_id=cl.ID
original_cluster_shape_input_prod,deproj_cluster_shape_input_prod,gabor_prod,unsharp_prod,attr_seg_map_prod,cls_stamp_prod=pipeline.do_morphometric_input_products.run(image,
cluster=cl,
image_id=image_id,
image_bkg_value=image.valid_flatten.min(),
cluster_th_level=cluster_th_level)
#Morphometrics features are extracted from the products
analysis_prod_collection.add_product(cls_stamp_prod)
analysis_prod_collection.add_product(attr_seg_map_prod)
morphometric_features_analysis_products_collection=pipeline.do_morphometric_features_extraction.run(image,
morphometry_input_data_original=original_cluster_shape_input_prod,
morphometry_input_data_deproj=deproj_cluster_shape_input_prod,
morphometry_input_data_gabor=gabor_prod,
morphometry_input_data_unsharp=unsharp_prod,
image_id=image_id,
cl_id=cl_id,
x_c=x_c,
y_c=y_c)
morph_feat=morphometric_features_analysis_products_collection.get_product_by_name('morph_features')
#print(type(morph_feat.array_values),morph_feat.array_values)
if len(cluster_list)==1 or ID==0:
out_prod=morph_feat
else:
out_prod.append_row(morph_feat.array_values)
analysis_prod_collection.add_product(out_prod)
return analysis_prod_collection
[docs]class MorphometricFeatureExtractionPipeline(AnalysisPipeline):
"""
:class:`.AnalysisPipeline` class for the Morphometric Feature Extraction Pipeline. The following processes are glued
by the pipeline:
- do_src_detection :class:`.DoSrcDetectionProcess`
- do_morphometric_input_products :class:`.DoMorphometricInputProducts`
- do_morphometric_features_extraction :class:`.DoMorphometricFeaturesExtraction`
Parameters
----------
name : str
the name for the Process
func : :func:
The function that handles tha pipeline algorithm
image_id : int
id of the image
plot_func : :func:
plotting function for this process
parser :
argv :
conf_file:
"""
def __init__(self,name='morph_features_script',func=do_morphometric_feature_extraction_pipeline_func,plot_func=analysis_plot,parser=None,argv=None,conf_file=None):
super(MorphometricFeatureExtractionPipeline,self).__init__(name,func,plot_func=analysis_plot,parser=parser,argv=argv,conf_file=conf_file)
self.add_analysis_process(DoSrcDetectionProcess,'do_src_detection' )
self.add_analysis_process(DoMorphometricInputProducts,'do_morphometric_input_products' )
self.add_analysis_process(DoMorphometricFeaturesExtraction,'do_morphometric_features_extraction')
