Source code for asterism.analysis_processes.morphometric_feature_extraction
"""
Overview
--------
This modules provides the implementation of the :class:`.DoMorphometricFeaturesExtraction` class
used to handle the process for the morphometric features extraction.
The tasks in the process are orchestrated by the :func:`.do_morphometric_features_extraction_process_func`
Classes relations
---------------------------------------
.. figure::
:align: center
Classes and Inheritance Structure
----------------------------------------------
.. inheritance-diagram:: asterism.analysis_processes.morphometric_feature_extraction.DoMorphometricFeaturesExtraction
Summary
---------
.. autosummary::
do_morphometric_features_extraction_process_func
FeaturesArray
DoMorphometricFeaturesExtraction
Module API
-----------
"""
from __future__ import division, absolute_import, print_function
from ..pipeline_manager.analysis_processes import AnalysisProcess
from asterism.pipeline_manager.analysis_products import *
from ..analysis_tasks.morphometry_features.extract_geometrical_features import DoExtractGeometricFeatures
from ..analysis_tasks.morphometry_features.extract_Hu_moments_features import DoExtractHuMomentsFeatures
from ..analysis_tasks.morphometry_features.extract_galaxy_profile_fit_features import DoExtractGalaxyProfileFitFeatures
from ..analysis_tasks.morphometry_features.extract_attr_polar_distr_features import DoExtractAttractorsRadialDistrFeatures
from ..analysis_tasks.morphometry_features.extract_morphology_features import DoExtractMorphologyFeatures
from ..core.morphometry.features import MorphometricFeatures,MorphometricFeaturesArray
from ..plotting.plot_tools import analysis_plot
import numpy as np
__author__ = 'andrea tramacere'
[docs]def do_morphometric_features_extraction_process_func(process,
image,
image_id=None,
cl_id=None,
x_c=None,
y_c=None,
morphometry_input_data_original=None,
morphometry_input_data_gabor=None,
morphometry_input_data_deproj=None,
morphometry_input_data_unsharp=None,
no_plot=False,
bkg_image=None,
bkg_lvl=None):
"""
Function for the morphometric feature extraction Process. The following :class:`.AnalysisTask` derived tasks are used
- extract_geometric_features :class:`.DoExtractGeometricFeatures`
- extract_Hu_moments_features :class:`.DoExtractHuMomentsFeatures`
- extract_morphological_features :class:`.DoExtractMorphologyFeatures`
- extract_galaxy_profile_fit_features :class:`.DoExtractGalaxyProfileFitFeatures`
- extract_arr_radial_distr_features :class:`.DoExtractAttractorsRadialDistrFeatures`
Features are from each task are returned as list of :class:`asterism.core.morphometry.features.MorphometricFeatures` objects
Each task function is calling feature extraction function from `asterism.core.morphometry`. These functions
have an internal try/execpt structure organinze in a such way that if a feture extraction fails, np.nan array
is returned, with the corresponding columns names
Parameters
----------
process : :class:`.AnalysisProcess`
instance of the analysis process
image : :class:`.Image` instance
The input image
image_id : int
id of the image
no_plo :t bool, optional (defaule=False):
morphometry_input_data_original :class:`asterism.analysis_processes.morphometric_features_input_products.MorphometryInputData`
class instance storing the input data for the morphometric feature extraction
morphometry_input_data_deproj :class:`asterism.analysis_processes.morphometric_features_input_products.MorphometryInputData`
class instance storing the input data for the morphometric feature extraction
bkg_image : 2D np.array, optional
numpy array of the image of the bkg image
bkg_lvl : float,optional
value of the background image, estimated for the current image
Returns
-------
products : :class:`AnalysisProcessProducts`
instance of the :class:`AnalysisProcessProducts` storing into the member prod_list :class:`FeaturesArray` instance
with all the features and features names extracted
"""
fig=None
fig_name=None
tasks_list=[process.extract_geometric_features,
process.extract_Hu_moments_features,
process.extract_morphological_features,
process.extract_galaxy_profile_fit_features,
process.extract_arr_radial_distr_features]
#list of MorphometricFeatures objs
if image_id is None:
image_id=0
if cl_id is None:
cl_id=0
if x_c is None:
x_c=-1.0
if y_c is None:
y_c=-1.0
features_list=[MorphometricFeatures(group_name='id',names=['image','cluster'],values=[image_id,cl_id+1],dtypes=[np.int64,np.int64])]
features_list.append(MorphometricFeatures(group_name='det_coord',names=['x','y'],values=[x_c,y_c],dtypes=[np.float32,np.float32]))
morphometric_features_array=MorphometricFeaturesArray(features_list)
for task in tasks_list:
if task.get_par_value('extract') == True:
features_list.extend(task.run(prod_original=morphometry_input_data_original,
prod_mapped_to_circle=morphometry_input_data_deproj,
gabor_prod=morphometry_input_data_gabor,
unsharp_prod=morphometry_input_data_unsharp,
image_id=image_id))
print(task,len(features_list))
morphometric_features_array.add(features_list)
analysis_products_collection=AnalysisProductsCollection()
analysis_products_collection.add_product(AnalysisProductRecArray(morphometric_features_array.values_tuple,morphometric_features_array.dtype, name='morph_features'))
return analysis_products_collection
[docs]class DoMorphometricFeaturesExtraction(AnalysisProcess):
"""
Derived class orchestrating the tasks
- extract_geometric_features :class:`.DoExtractGeometricFeatures`
- extract_Hu_moments_features :class:`.DoExtractHuMomentsFeatures`
- extract_morphological_features :class:`.DoExtractMorphologyFeatures`
- extract_galaxy_profile_fit_features :class:`.DoExtractGalaxyProfileFitFeatures`
- extract_arr_radial_distr_features :class:`.DoExtractAttractorsRadialDistrFeatures`
Parameters
----------
name : str
the name for the Process
func : :function:
The function that handles tha tasks
image_id : int
id of the image
plot_func : :function:
plotting function for this process
parser :
add_plot_task : bool
"""
def __init__(self,name='do_gal_shape_extraction',func=do_morphometric_features_extraction_process_func,plot_func=analysis_plot,parser=None,add_plot_task=True):
super(DoMorphometricFeaturesExtraction,self).__init__(name,func,plot_func=plot_func,parser=parser,add_plot_task=add_plot_task)
self.add_analysis_task(DoExtractGeometricFeatures, 'extract_geometric_features')
self.add_analysis_task(DoExtractHuMomentsFeatures, 'extract_Hu_moments_features')
self.add_analysis_task(DoExtractMorphologyFeatures, 'extract_morphological_features')
self.add_analysis_task(DoExtractGalaxyProfileFitFeatures, 'extract_galaxy_profile_fit_features')
self.add_analysis_task(DoExtractAttractorsRadialDistrFeatures, 'extract_arr_radial_distr_features')
