i.pca: added tests for the module #3550

HamedElgizery · 2024-04-01T19:56:31Z

This PR adds a test suite using gunittest for the i.pca module.

i.pca is tested against the sample data used in CI.

The expected results (from r.info and r.univar) are saved in the data directory, and are used to validate the correctness of the module.

imagery/i.pca/testsuite/test_pca.py

ninsbl

Thanks! In general, this looks very good, and I know it is more than skill-tests for GSoC in other projects.
Nevertheless, I made some suggestions for changes, Please have a look at them.

Most importantly, please re-format the added Pyhton file using black. See: https://github.com/OSGeo/grass/actions/runs/8512975348/job/23315779012#step:8:257 for how it is used in CI. If the file does not comply to black formating standards for Python, CI will fail and the PR cannot be merged,

You can install black with: pip install black==23.1.0

imagery/i.pca/testsuite/data/lsat7_2002_pca_1_univar.out

imagery/i.pca/testsuite/test_pca.py

HamedElgizery · 2024-04-02T00:26:20Z

@ninsbl
I have updated the script, reformatted it with black, and removed the data directory.

ninsbl

Looks good to me...

imagery/i.pca/testsuite/test_pca.py

neteler · 2024-04-02T10:01:52Z

I just tried it locally, runs ok but yields a SyntaxWarning: invalid escape sequence in line 39:

GRASS nc_spm_08_grass7/user1:testsuite > python test_pca.py 
/home/mneteler/software/grass_main/imagery/i.pca/testsuite/test_pca.py:39: SyntaxWarning: invalid escape sequence '\,'
  lsat7_2002_pca_info_out = """north=228513
PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]
PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]
PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]
PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]
PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]
PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]

Computing covariance matrix...
 100%
Calculating principal components...
 100%
Rescaling to range 0,255...
 100%
Eigen values, (vectors), and [percent importance]:

.
----------------------------------------------------------------------
Ran 1 test in 4.239s
OK

lucadelu · 2024-04-02T10:27:23Z

I didn't get it with python 3.11

GRASS nc_spm_08_grass7/user1:~ > python /tmp/test_pca.py 
PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]
PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]
PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]
PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]
PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]
PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]

Computing covariance matrix...
 100%
Calculating principal components...
 100%
Rescaling to range 0,255...
 100%
Eigen values, (vectors), and [percent importance]:

.
----------------------------------------------------------------------
Ran 1 test in 2.570s
OK

nilason · 2024-04-02T10:39:08Z

I just tried it locally, runs ok but yields a SyntaxWarning: invalid escape sequence in line 39:

GRASS nc_spm_08_grass7/user1:testsuite > python test_pca.py 
/home/mneteler/software/grass_main/imagery/i.pca/testsuite/test_pca.py:39: SyntaxWarning: invalid escape sequence '\,'
  lsat7_2002_pca_info_out = """north=228513
PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]

This is likely a Python 3.12 issue.

Markus, please test with adding an r before triple quote (file test_pca.py:39):

 lsat7_2002_pca_info_out = r"""north=228513

neteler · 2024-04-02T12:14:29Z

Yes, python 3.12 here:

python --version
Python 3.12.2

The warning then disappears but it then fails:

GRASS nc_spm_08_grass7/user1:testsuite > python test_pca.py
PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]
PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]
PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]
PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]
PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]
PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]

Computing covariance matrix...
 100%
Calculating principal components...
 100%
Rescaling to range 0,255...
 100%
Eigen values, (vectors), and [percent importance]:

F
======================================================================
FAIL: test_pca_sample (__main__.TestReport.test_pca_sample)
Testing pca sample
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/mneteler/software/grass_main/imagery/i.pca/testsuite/test_pca.py", line 153, in test_pca_sample
    self.assertRasterFitsInfo(
  File "/home/mneteler/software/grass_main/dist.x86_64-pc-linux-gnu/etc/python/grass/gunittest/case.py", line 315, in assertRasterFitsInfo
    self.assertModuleKeyValue(
  File "/home/mneteler/software/grass_main/dist.x86_64-pc-linux-gnu/etc/python/grass/gunittest/case.py", line 271, in assertModuleKeyValue
    self.fail(self._formatMessage(msg, stdMsg))
AssertionError: r.info map=lsat7_2002_pca.1 -g -r -e difference:
mismatch values (key, reference, actual): [('comments', ['\\"Eigen values', '(vectors)', 'and [percent importance]:PC1   4334.35 ( 0.2824', 0.3342, 0.5092, -0.0087, 0.5264, '0.5217) [83.04%]PC2    588.31 ( 0.2541', 0.1885, 0.2923, -0.7428, -0.511, '-0.0403) [11.27%]PC3    239.22 ( 0.3801', 0.3819, 0.2681, 0.6238, -0.4, '-0.2980) [ 4.58%]PC4     32.85 ( 0.1752', -0.0191, -0.4053, 0.1593, -0.4435, '0.7632) [ 0.63%]PC5     20.73 (-0.6170', -0.2514, 0.6059, 0.1734, -0.3235, '0.2330) [ 0.40%]PC6      4.08 (-0.5475', 0.8021, -0.2282, -0.0607, -0.0208, '0.0252) [ 0.08%]i.pca input=\\"lsat7_2002_10', 'lsat7_2002_20', 'lsat7_2002_30', 'lsat7_2002_40\\', 'lsat7_2002_50', 'lsat7_2002_70\\" output=\\"lsat7_2002_pca\\" rescale=0', '255 \\percent=99"'], ['"Eigen values', '(vectors)', 'and [percent importance]:PC1   4334.35 ( 0.2824', 0.3342, 0.5092, -0.0087, 0.5264, '0.5217) [83.04%]PC2    588.31 ( 0.2541', 0.1885, 0.2923, -0.7428, -0.511, '-0.0403) [11.27%]PC3    239.22 ( 0.3801', 0.3819, 0.2681, 0.6238, -0.4, '-0.2980) [ 4.58%]PC4     32.85 ( 0.1752', -0.0191, -0.4053, 0.1593, -0.4435, '0.7632) [ 0.63%]PC5     20.73 (-0.6170', -0.2514, 0.6059, 0.1734, -0.3235, '0.2330) [ 0.40%]PC6      4.08 (-0.5475', 0.8021, -0.2282, -0.0607, -0.0208, '0.0252) [ 0.08%]i.pca input="lsat7_2002_10', 'lsat7_2002_20', 'lsat7_2002_30', 'lsat7_2002_40\\', 'lsat7_2002_50', 'lsat7_2002_70" output="lsat7_2002_pca" rescale=0', '255 \\percent=99"'])]
command: r.info map=lsat7_2002_pca.1 -g -r -e {'map': 'lsat7_2002_pca.1', 'flags': 'gre'}

----------------------------------------------------------------------
Ran 1 test in 1.190s
FAILED (failures=1)

HamedElgizery · 2024-04-02T12:36:33Z

The warning then disappears but it then fails:

GRASS nc_spm_08_grass7/user1:testsuite > python test_pca.py
PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]
PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]
PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]
PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]
PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]
PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]

Computing covariance matrix...
 100%
Calculating principal components...
 100%
Rescaling to range 0,255...
 100%
Eigen values, (vectors), and [percent importance]:

F
======================================================================
FAIL: test_pca_sample (__main__.TestReport.test_pca_sample)
Testing pca sample
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/mneteler/software/grass_main/imagery/i.pca/testsuite/test_pca.py", line 153, in test_pca_sample
    self.assertRasterFitsInfo(
  File "/home/mneteler/software/grass_main/dist.x86_64-pc-linux-gnu/etc/python/grass/gunittest/case.py", line 315, in assertRasterFitsInfo
    self.assertModuleKeyValue(
  File "/home/mneteler/software/grass_main/dist.x86_64-pc-linux-gnu/etc/python/grass/gunittest/case.py", line 271, in assertModuleKeyValue
    self.fail(self._formatMessage(msg, stdMsg))
AssertionError: r.info map=lsat7_2002_pca.1 -g -r -e difference:
mismatch values (key, reference, actual): [('comments', ['\\"Eigen values', '(vectors)', 'and [percent importance]:PC1   4334.35 ( 0.2824', 0.3342, 0.5092, -0.0087, 0.5264, '0.5217) [83.04%]PC2    588.31 ( 0.2541', 0.1885, 0.2923, -0.7428, -0.511, '-0.0403) [11.27%]PC3    239.22 ( 0.3801', 0.3819, 0.2681, 0.6238, -0.4, '-0.2980) [ 4.58%]PC4     32.85 ( 0.1752', -0.0191, -0.4053, 0.1593, -0.4435, '0.7632) [ 0.63%]PC5     20.73 (-0.6170', -0.2514, 0.6059, 0.1734, -0.3235, '0.2330) [ 0.40%]PC6      4.08 (-0.5475', 0.8021, -0.2282, -0.0607, -0.0208, '0.0252) [ 0.08%]i.pca input=\\"lsat7_2002_10', 'lsat7_2002_20', 'lsat7_2002_30', 'lsat7_2002_40\\', 'lsat7_2002_50', 'lsat7_2002_70\\" output=\\"lsat7_2002_pca\\" rescale=0', '255 \\percent=99"'], ['"Eigen values', '(vectors)', 'and [percent importance]:PC1   4334.35 ( 0.2824', 0.3342, 0.5092, -0.0087, 0.5264, '0.5217) [83.04%]PC2    588.31 ( 0.2541', 0.1885, 0.2923, -0.7428, -0.511, '-0.0403) [11.27%]PC3    239.22 ( 0.3801', 0.3819, 0.2681, 0.6238, -0.4, '-0.2980) [ 4.58%]PC4     32.85 ( 0.1752', -0.0191, -0.4053, 0.1593, -0.4435, '0.7632) [ 0.63%]PC5     20.73 (-0.6170', -0.2514, 0.6059, 0.1734, -0.3235, '0.2330) [ 0.40%]PC6      4.08 (-0.5475', 0.8021, -0.2282, -0.0607, -0.0208, '0.0252) [ 0.08%]i.pca input="lsat7_2002_10', 'lsat7_2002_20', 'lsat7_2002_30', 'lsat7_2002_40\\', 'lsat7_2002_50', 'lsat7_2002_70" output="lsat7_2002_pca" rescale=0', '255 \\percent=99"'])]
command: r.info map=lsat7_2002_pca.1 -g -r -e {'map': 'lsat7_2002_pca.1', 'flags': 'gre'}

----------------------------------------------------------------------
Ran 1 test in 1.190s
FAILED (failures=1)

It is probably because of the quotations inside the string...

Can you try to change the variable "lsat7_2002_pca_info_out" to:

    lsat7_2002_pca_info_out = r"""north=228513
        south=214975.5
        east=645012
        west=629992.5
        nsres=28.5
        ewres=28.5
        rows=475
        cols=527
        cells=250325
        datatype=CELL
        ncats=0
        comments="Eigen values, (vectors), and [percent importance]:PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]i.pca input="lsat7_2002_10,lsat7_2002_20,lsat7_2002_30,lsat7_2002_40\,lsat7_2002_50,lsat7_2002_70" output="lsat7_2002_pca" rescale=0,255 \percent=99" """

nilason · 2024-04-02T12:46:13Z

diff --git a/imagery/i.pca/testsuite/test_pca.py b/imagery/i.pca/testsuite/test_pca.py
index 9da7991f87..7999feba8e 100644
--- a/imagery/i.pca/testsuite/test_pca.py
+++ b/imagery/i.pca/testsuite/test_pca.py
@@ -36,7 +36,7 @@ class TestReport(TestCase):
             output="lsat7_2002_pca",
         )
 
-        lsat7_2002_pca_info_out = """north=228513
+        lsat7_2002_pca_info_out = r"""north=228513
             south=214975.5
             east=645012
             west=629992.5
@@ -47,7 +47,7 @@ class TestReport(TestCase):
             cells=250325
             datatype=CELL
             ncats=0
-            comments=\"Eigen values, (vectors), and [percent importance]:PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]i.pca input=\"lsat7_2002_10,lsat7_2002_20,lsat7_2002_30,lsat7_2002_40\,lsat7_2002_50,lsat7_2002_70\" output=\"lsat7_2002_pca\" rescale=0,255 \percent=99" """
+            comments="Eigen values, (vectors), and [percent importance]:PC1   4334.35 ( 0.2824, 0.3342, 0.5092,-0.0087, 0.5264, 0.5217) [83.04%]PC2    588.31 ( 0.2541, 0.1885, 0.2923,-0.7428,-0.5110,-0.0403) [11.27%]PC3    239.22 ( 0.3801, 0.3819, 0.2681, 0.6238,-0.4000,-0.2980) [ 4.58%]PC4     32.85 ( 0.1752,-0.0191,-0.4053, 0.1593,-0.4435, 0.7632) [ 0.63%]PC5     20.73 (-0.6170,-0.2514, 0.6059, 0.1734,-0.3235, 0.2330) [ 0.40%]PC6      4.08 (-0.5475, 0.8021,-0.2282,-0.0607,-0.0208, 0.0252) [ 0.08%]i.pca input="lsat7_2002_10,lsat7_2002_20,lsat7_2002_30,lsat7_2002_40\,lsat7_2002_50,lsat7_2002_70" output="lsat7_2002_pca" rescale=0,255 \percent=99" """
 
         lsat7_2002_pca_univar_out = [
             """n=250325

works for both 3.12 and 3.11.

HamedElgizery added 5 commits April 1, 2024 03:23

Add test_pca.py

874e926

Add assertRasterFitsInfo assertion

5390572

Add tests for r.univar results [i.pca] & save expected results in files

57141c9

i.pca: clear maps after testing is done

2dea343

Add header to test_pca.py

9c7ff81

HamedElgizery mentioned this pull request Apr 1, 2024

Add tests to i.modis, i.landsat, i.sentinel download OSGeo/grass-addons#1033

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remove data directory and save results in script

d2503b5

HamedElgizery force-pushed the i.pca.testsuite branch from 7e78d16 to d2503b5 Compare April 2, 2024 00:12

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ninsbl dismissed their stale review via c5e3795 April 2, 2024 06:52

ninsbl added 2 commits April 2, 2024 08:52

Update imagery/i.pca/testsuite/test_pca.py

c5e3795

Merge branch 'main' into i.pca.testsuite

db94317

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ninsbl merged commit 315f7ef into OSGeo:main Apr 2, 2024
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i.pca: added tests for the module #3550

i.pca: added tests for the module #3550

HamedElgizery commented Apr 1, 2024

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nilason commented Apr 2, 2024

i.pca: added tests for the module #3550

i.pca: added tests for the module #3550

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