Add PSFMap class #1432

registerrier · 2018-06-18T14:38:52Z

This PR adds a function to project a gammapy.irf.PSF3D on a gammapy.map.
It also adds a class to work with the resulting Map to extract an gammapy.irf.EnergyDependentTablePSF at any position or to produce a PSF kernel following the implementation of PR #1388.
The complete computation of a PSFMap for a collection of observation has to be performed on a higher level maker class. This will be added in a coming PR.

cdeil

@registerrier - Thanks!

I've left some inline comments.

More generally, I think extending the class-level docstring a bit to describe what this is would be useful.
An example code snippet how to make one of those things in an Examples section is always gold for users and developers, because then they can just copy & paste that and start to learn / try out a new class in ipython / Jupyter. In this case it could be possible to read a CTA PSF IRF and make such a map with ~ 5 lines?

The other main comment I have is the name. You called the class PSFMap. But is is not a map. It has a map. Looking at how this is used then from callers, you get code like in your test:

pmap = PSFMap(psfmap)

It's easy to be confused in calling code what the "psf_map" and the "pmap" are, no?
As you've probably seen in
https://github.com/gammapy/gammapy/pull/1388/files#diff-cde80870ee7dc037d5c9a8863a870762R15
I put "kernel" in the class name, because for me a fundamental difference wrt the IRF classes is that those represent probability density functions, but this is a discretised probability mass function, i.e. what is commonly called a "kernel".
Suggest to avoid the use of "Map" in the class name here to avoid confusion.

cdeil · 2018-06-19T06:34:44Z

gammapy/cube/psf_map.py

@@ -0,0 +1,189 @@
+import numpy as np


For new files, always add the two boilerplate lines at the top: license and future inits (copy from any other file).
Same for the new test file you're adding here.

cdeil · 2018-06-19T06:36:54Z

gammapy/cube/psf_map.py

+    'PSFMap'
+]
+
+def make_psf3d(psf_analytical, rad):


Suggest to attach this converted as a to_psf3d method on EnergyDependentMultiGaussPSF.

As a standalone function it's hard to find, and the name make_psf3d doesn't capture well that this is really convert_energy_dependent_multi_gauss_psf_to_psf_3d.

Good point.
I have moved make_psf3d to EnergyDependentMultiGaussPSF.to_psf3d.

cdeil · 2018-06-19T06:38:08Z

gammapy/cube/psf_map.py

+    rad : `~astropy.unit.Quantity` or `~astropy.coordinates.Angle`
+        the array of position errors (rad) on which the PSF3D will be defined
+
+    Return


Returns with an s.

Please check once locally that python setup.py build_docs works and the resulting HTML docs formatting is OK for the new functions / classes you're adding.

cdeil · 2018-06-19T06:38:52Z

gammapy/cube/psf_map.py

+    ----------
+    psf_analytical : `~gammapy.irf.EnergyDependentMultiGaussPSF`
+        the analytical PSF to be transformed to PSF3D
+    rad : `~astropy.unit.Quantity` or `~astropy.coordinates.Angle`


units with an s.

cdeil · 2018-06-19T06:41:08Z

gammapy/cube/psf_map.py

+    valid = np.where(separations < max_offset)
+
+    # Compute PSF values
+    psf_values = np.transpose(psf.evaluate(offset=separations[valid], energy=energy, rad=rad), axes=(2, 0, 1))


Suggest to put the transpose call on the next line.
Very long lines are hard to read, and also harder to debug if one ever needs to enter a debugger here.

cdeil · 2018-06-19T07:00:57Z

gammapy/cube/psf_map.py

+        normalize : bool
+            normalize PSF per energy bin.
+        factor : int
+            oversampling factor to compute the PSF


Add empty line before Returns section.

cdeil · 2018-06-19T07:01:31Z

gammapy/cube/psf_map.py

+        return EnergyDependentTablePSF(energy=self.energies,rad=self.rad,psf_value=psf_values.T)
+
+    def get_psf_kernel(self, position, npix, pixel_size, normalize=True, factor=5):
+        """Returns a PSF kernel at the given position.


Always add empty line after the first summary line in a docstring. Then the docs appear nicely in the method summary overview.

cdeil · 2018-06-19T07:02:21Z

gammapy/cube/psf_map.py

+        Parameters
+        ----------
+        fraction : float
+            the containment fraction (a positive number <=1). Default 0.68.


Add empty line before Returns section.

cdeil · 2018-06-19T07:06:28Z

gammapy/cube/tests/test_psf_map.py

+    psfmap = make_psf_map(psf, pointing, geom, 3*u.deg)
+
+    pmap = PSFMap(psfmap)
+    # need to assert something...


Yes, please execute each method (especially get_energy_dependent_table_psf) and add an assert on the output.

cdeil · 2018-06-19T07:10:46Z

gammapy/cube/psf_map.py

+    return psfmap
+
+
+class PSFMap():


Write class PSFMap(object).

If you omit the object you'll get an "old-style class" on Python 2. Usually you don't notice, but really those old-style classes should not be used since Python 2.1 or something like that, and then in some cases they do behave in weird ways.

registerrier · 2018-06-19T14:27:45Z

Regarding the name, indeed PSFMapis not very satisfactory since it is not a Map. Yet the only thing it contains is a Map. The class mostly provides convenience methods to interact with the map of PSFs, such as the extraction of an EnergyDependentTablePSFat any position. A possibility could be to have only functions taking the actual Map as argument. But this seemed an easier solution for users.

Making an inheritance on Map did not seem like a good idea since the Map could be an WcsNDMapor an HpxNDMap and it is expected to have specific axes.

This object does not contain kernels a priori, but can be used to create them. It could be called PSFKernelMaker or PSFKernelFactory or?

What we are doing here is really to create and handle maps of IRFs (here PSF but the approach would be nearly identical for Edisp). So PSFMapHandler could be a better name?

cdeil · 2018-06-19T19:29:38Z

@registerrier - You're right. I was confusing this PSFMap object with what I started to implement in #1388, a real PSF kernel array where I also used a Map object to hold it.

I'm afraid I'm out of good ideas concerning the name. Maybe leave as-is? I certainly didn't want to suggest changing to subclassing or something like that, I was just confused about what this is and was thinking if there is a better name.

… of PSF and a class to interact with it

…al.py (e.g. missing imports)

cdeil · 2018-07-05T12:35:18Z

gammapy/cube/psf_map.py

+            raise ValueError("EnergyDependentTablePSF can be extracted at one single position only.")
+
+        # axes ordering fixed. Could be changed.
+        pix_ener = np.arange(self.psf_map.geom.axes[1].nbin)


Suggest to pick fixed names and always access axes by name, not position index.

cdeil

Some quick comments inline.
I'll try this out locally now ...

cdeil · 2018-07-05T12:38:14Z

gammapy/cube/tests/test_psf_map.py

+    assert psf_map.geom.axes[0] == rad_axis
+    assert psf_map.geom.axes[1] == energy_axis
+
+    # Check unit


Suggest to remove such comment lines as "check unit", that don't add any extra info.
Please look over the diff and remove such comment lines.

cdeil · 2018-07-05T12:43:17Z

gammapy/cube/psf_map.py

+        table_psf = self.get_energy_dependent_table_psf(position)
+        return PSFKernel.from_table_psf(table_psf, geom, max_radius, factor)
+
+    def containment_radius_map(self, fraction = 0.68):


How much work is it to implement the containment radius map?
Would be very nice to have, no?
Alternatively, please open an issue for this and label it beginner friendly and we'll try to find soemone to do it next week.

cdeil · 2018-07-10T21:01:04Z

@registerrier - Thanks!

registerrier self-assigned this Jun 18, 2018

registerrier added the feature label Jun 18, 2018

registerrier added this to To do in gammapy.maps via automation Jun 18, 2018

registerrier added this to the 0.8 milestone Jun 18, 2018

registerrier requested review from cdeil and adonath June 18, 2018 14:39

cdeil mentioned this pull request Jun 19, 2018

Add a PSF map kernel class #1388

Closed

cdeil suggested changes Jun 19, 2018

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registerrier moved this from To do to In progress in gammapy.maps Jun 20, 2018

registerrier added 14 commits July 5, 2018 12:02

Initial commit of psf_map.py which contains functions to create a Map…

ef40054

… of PSF and a class to interact with it

Updated code

729c36f

Added a method to extract a kernel from a PSFMap

7e7e3c0

added import in __init__

30bb339

Add test for psf map

d9cde0d

moved make_psf3D function to EnergyDependentMultiGaussPSF.to_psf3d

3d76769

moved make_psf3D function to EnergyDependentMultiGaussPSF.to_psf3d

7eb7c25

removed make_psf3d from __all__ and small corrections in psf_analytic…

edfa21a

…al.py (e.g. missing imports)

added missing imports and license comment

84c9116

split long line in make_psf_map

98d2733

cleaned members of PSFMap class

ff1b2f7

Adapted PSFMap to the new PSFKernel and added tests

160c3ff

Changed from_file to read. Added write method and added associated tests

7e476d8

Some corrections and resolution of merge conflict

79a6e51

registerrier force-pushed the irf_map branch from 851459b to 79a6e51 Compare July 5, 2018 10:26

registerrier added 2 commits July 5, 2018 14:25

Detailed code example

7515105

PEP8

8f334e5

cdeil reviewed Jul 5, 2018

View reviewed changes

corrected raise

3b67ce6

cdeil reviewed Jul 5, 2018

View reviewed changes

Added get_psf_kernel test and code cleanup

f1d1954

registerrier mentioned this pull request Jul 6, 2018

Improve SkyModelMapFit #1454

Merged

registerrier added 3 commits July 9, 2018 09:56

access PSFMap data through properties

0a5a3ba

Cleaned version

9622dc1

Added tests for EnergyDependentMultiGaussPSF.to_psf3d()

df1508f

cdeil assigned cdeil and unassigned registerrier Jul 10, 2018

Small cleanup to PSFMap

63b7a99

cdeil approved these changes Jul 10, 2018

View reviewed changes

cdeil merged commit 2f9afdf into gammapy:master Jul 10, 2018

gammapy.maps automation moved this from In progress to Done Jul 10, 2018

cdeil changed the title ~~Add functions and class to work with PSFs with gammapy.maps~~ Add PSFMap class Aug 15, 2018

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Add PSFMap class #1432

Add PSFMap class #1432

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Add PSFMap class #1432

Add PSFMap class #1432

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registerrier commented Jun 19, 2018

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cdeil commented Jul 10, 2018