Create a Python wrapper

.gitignore

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+[Bb]uild
+__pycache__

python/test.py

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+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file %filename%.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 22 mars 2018
+#
+# TODO details
+
+import triskele
+import numpy as np
+
+A = np.arange(10*10).reshape(10,10)
+
+t = triskele.Triskele(A)
+print (t.filter())

python/triskele/Triskele.py

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+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+# \file Triskele.py
+# \brief TODO
+# \author Florent Guiotte <florent.guiotte@gmail.com>
+# \version 0.1
+# \date 22 mars 2018
+#
+# TODO details
+
+import os
+import subprocess
+from pathlib import Path
+import numpy as np
+import libtiff
+
+class Triskele:
+    def __init__(self, raster, dtype=np.uint8, cache_dir='/tmp', verbose=True):
+
+        self.verbose = verbose
+        self.triskele_bin = Path(os.path.dirname(os.path.realpath(__file__))\
+                + '/../../build/out/apGenerator')
+        self.cache_dir = Path(cache_dir)
+
+        if not self.triskele_bin.exists():
+            raise EnvironmentError ('TRISKELE bin not found: {}'.format(self.triskele_bin))
+
+        if not self.cache_dir.exists():
+            raise EnvironmentError ('Cache directory not found: {}'.format(self.cache_dir))
+
+        self.infile  = self.cache_dir.joinpath('infile.tif')
+        self.outfile = self.cache_dir.joinpath('outfile.tif')
+
+        self.areafile = self.cache_dir.joinpath('areafile.txt')
+        self.sdfile   = self.cache_dir.joinpath('sdfile.txt')
+        self.moifile  = self.cache_dir.joinpath('moifile.txt')
+
+        self._write_infile(raster, dtype)
+
+    def filter(self, tree='max-tree', area=None, standard_deviation=None, moment_of_inertia=None):
+        self._setup(tree, area, standard_deviation, moment_of_inertia)
+        self._run()
+        return self._read_outfile()
+
+    def _read_outfile(self):
+        return libtiff.TIFF.open(self.outfile).read_image()
+
+    def _write_infile(self, raster, dtype):
+        ## Scale to new dtype
+        rep = np.iinfo(dtype)
+
+        raster = raster.astype(np.float32)
+        raster -= raster.min() - rep.min
+        raster *= (rep.max - rep.min) / (raster.max() - raster.min())
+        raster = raster.astype(dtype)
+
+        tif = libtiff.TIFFimage(raster, description='TRISKELE Python wrapper')
+        tif.write_file(self.infile, verbose=self.verbose, compression=None) # 'lzw'
+
+    def _setup(self, tree, area, standard_deviation, moment_of_inertia):
+        self.process = [self.triskele_bin,
+                '-i', '{}'.format(self.infile),
+                '-o', '{}'.format(self.outfile),
+                '--{}'.format(tree)]
+
+        if area is not None:
+            np.savetxt(self.areafile, area, fmt='%d')
+            self.process.extend(['--area', '{}'.format(self.areafile)])
+
+        if standard_deviation is not None:
+            np.savetxt(self.sdfile, standard_deviation, fmt='%f')
+            self.process.extend(['--standard-deviation', '{}'.format(self.sdfile)])
+
+        if moment_of_inertia is not None:
+            np.savetxt(self.moifile, moment_of_inertia, fmt='%f')
+            self.process.extend(['--moment-of-inertia', '{}'.format(self.moifile)])
+
+    def _run(self):
+
+        tryskele = subprocess.Popen(self.process, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        if self.verbose:
+            print('STDOUT:\n' + tryskele.stdout.read().decode() + \
+                    '\nSTDERR:\n' + tryskele.stderr.read().decode())

python/triskele/__init__.py

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+from .Triskele import Triskele