diff --git a/km3io/daq.py b/km3io/daq.py
index eb12052b6070852852c6d8bf7dc61714ecc26b7d..e1f1e55ca5001766d54e1a21d80a9430eb3b0047 100644
--- a/km3io/daq.py
+++ b/km3io/daq.py
@@ -30,9 +30,10 @@ def get_rate(value):
return MINIMAL_RATE_HZ * np.exp(value * RATE_FACTOR)
-@nb.guvectorize(
- "void(i8, b1[:], b1[:])", "(), (n) -> (n)", target="parallel", nopython=True
- )
+@nb.guvectorize("void(i8, b1[:], b1[:])",
+ "(), (n) -> (n)",
+ target="parallel",
+ nopython=True)
def unpack_bits(value, bits_template, out):
"""Return a boolean array for a value's bit representation.
diff --git a/km3io/offline.py b/km3io/offline.py
index 362d90d69311cd587706ce71f2e3211cac511994..8bd986d53834e73ff8d5a2f66e8080333c2462b6 100644
--- a/km3io/offline.py
+++ b/km3io/offline.py
@@ -5,7 +5,6 @@ import km3io.definitions.trigger
import km3io.definitions.fitparameters
import km3io.definitions.reconstruction
-
# 110 MB based on the size of the largest basket found so far in km3net
BASKET_CACHE_SIZE = 110 * 1024**2
@@ -178,7 +177,9 @@ class OfflineKeys:
list of all "trks.fitinf" keys.
"""
if self._fit_keys is None:
- self._fit_keys = sorted(self.fitparameters, key=self.fitparameters.get, reverse=False)
+ self._fit_keys = sorted(self.fitparameters,
+ key=self.fitparameters.get,
+ reverse=False)
# self._fit_keys = [*fit.keys()]
return self._fit_keys
@@ -377,13 +378,13 @@ class OfflineReader:
if b'Head;1' in fobj.keys():
self._header = {}
for n, x in fobj['Head']._map_3c_string_2c_string_3e_.items():
- print("{:15s} {}".format(n.decode("utf-8"), x.decode("utf-8")))
+ print("{:15s} {}".format(n.decode("utf-8"),
+ x.decode("utf-8")))
self._header[n.decode("utf-8")] = x.decode("utf-8")
if b'Header;1' in fobj.keys():
warnings.warn("Your file header has an unsupported format")
return self._header
-
@property
def keys(self):
"""wrapper for all keys in an offline file.
@@ -491,17 +492,21 @@ class OfflineReader:
"""
if self._best_reco is None:
keys = ", ".join(self.keys.fit_keys[:-1])
- empty_fit_info = np.array([match for match in
- self._find_empty(self.tracks.fitinf)])
- fit_info = [i for i,j in zip(self.tracks.fitinf,
- empty_fit_info[:,1]) if j is not None]
+ empty_fit_info = np.array(
+ [match for match in self._find_empty(self.tracks.fitinf)])
+ fit_info = [
+ i for i, j in zip(self.tracks.fitinf, empty_fit_info[:, 1])
+ if j is not None
+ ]
stages = self._get_max_reco_stages(self.tracks.rec_stages)
- fit_data = np.array([i[j] for i,j in zip(fit_info, stages[:,2])])
+ fit_data = np.array([i[j] for i, j in zip(fit_info, stages[:, 2])])
rows_size = len(max(fit_data, key=len))
- equal_size_data = np.vstack([np.hstack([i, np.zeros(rows_size-len(i))
- + np.nan]) for i in fit_data])
- self._best_reco = np.core.records.fromarrays(equal_size_data.transpose(),
- names=keys)
+ equal_size_data = np.vstack([
+ np.hstack([i, np.zeros(rows_size - len(i)) + np.nan])
+ for i in fit_data
+ ])
+ self._best_reco = np.core.records.fromarrays(
+ equal_size_data.transpose(), names=keys)
return self._best_reco
def _get_max_reco_stages(self, reco_stages):
@@ -522,12 +527,14 @@ class OfflineReader:
*lentgh of the maximum reco_stages
*position of the maximum reco_stages
"""
- empty_reco_stages = np.array([match for match in
- self._find_empty(reco_stages)])
- max_reco_stages = np.array([[max(i, key=len), len(max(i, key=len)),
- i.index(max(i, key=len))] for i,j in
- zip(reco_stages, empty_reco_stages[:,1])
- if j is not None])
+ empty_reco_stages = np.array(
+ [match for match in self._find_empty(reco_stages)])
+ max_reco_stages = np.array(
+ [[max(i, key=len),
+ len(max(i, key=len)),
+ i.index(max(i, key=len))]
+ for i, j in zip(reco_stages, empty_reco_stages[:, 1])
+ if j is not None])
return max_reco_stages
def get_reco_fit(self, stages):
@@ -555,17 +562,21 @@ class OfflineReader:
"""
keys = ", ".join(self.keys.fit_keys[:-1])
fit_info = self.tracks.fitinf
- rec_stages = np.array([match for match in
- self._find_rec_stages(stages)])
- if np.all(rec_stages[:,1]==None):
- raise ValueError("The stages {} are not found in your file."
- .format(str(stages)))
+ rec_stages = np.array(
+ [match for match in self._find_rec_stages(stages)])
+ if np.all(rec_stages[:, 1] == None):
+ raise ValueError(
+ "The stages {} are not found in your file.".format(
+ str(stages)))
else:
- fit_data = np.array([i[k] for i,j,k in zip(fit_info,
- rec_stages[:,0], rec_stages[:,1])
- if k is not None])
+ fit_data = np.array([
+ i[k]
+ for i, j, k in zip(fit_info, rec_stages[:, 0], rec_stages[:,
+ 1])
+ if k is not None
+ ])
rec_array = np.core.records.fromarrays(fit_data.transpose(),
- names=keys)
+ names=keys)
return rec_array
def _find_rec_stages(self, stages):
@@ -615,9 +626,9 @@ class OfflineReader:
"""
for i, rs in enumerate(array):
try:
- if len(rs)==0:
+ if len(rs) == 0:
j = None
- if len(rs)!=0:
+ if len(rs) != 0:
j = rs.index([])
except ValueError:
j = False # rs not empty but [] not found
@@ -784,11 +795,8 @@ class OfflineTracks:
return OfflineTrack(self._keys, [v[item] for v in self._values],
fitparameters=self._fitparameters)
else:
- return OfflineTracks(
- self._keys,
- [v[item] for v in self._values],
- fitparameters=self._fitparameters
- )
+ return OfflineTracks(self._keys, [v[item] for v in self._values],
+ fitparameters=self._fitparameters)
def __len__(self):
try:
@@ -831,8 +839,10 @@ class OfflineTrack:
"{:30} {:^2} {:>26}".format(k, ':', str(v))
for k, v in zip(self._keys, self._values) if k not in ['fitinf']
]) + "\n\t" + "\n\t".join([
- "{:30} {:^2} {:>26}".format(k, ':', str(getattr(self, 'fitinf')[v]))
- for k, v in self._fitparameters.items() if len(getattr(self, 'fitinf'))>v
+ "{:30} {:^2} {:>26}".format(k, ':', str(
+ getattr(self, 'fitinf')[v]))
+ for k, v in self._fitparameters.items()
+ if len(getattr(self, 'fitinf')) > v
]) # I don't like 18 being explicit here
def __getitem__(self, item):
diff --git a/requirements-dev.txt b/requirements-dev.txt
index ab7cf28580f2dcfbc3ee5f3fb1bd354853f9639e..25bd197c80c8c619fa392e662298066b8f72b4d9 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -10,4 +10,4 @@ sphinx-autoapi
sphinx-gallery
sphinx-rtd-theme
sphinxcontrib-versioning
-yapf
+yapf>=0.29.0
diff --git a/tests/test_offline.py b/tests/test_offline.py
index 281bf83d0f956a19f685b50fea25bba1f3a14c1b..5257b4d99b834f5a33f7624041ce145351e7d674 100644
--- a/tests/test_offline.py
+++ b/tests/test_offline.py
@@ -49,8 +49,10 @@ class TestOfflineKeys(unittest.TestCase):
def test_trigger(self):
# there are 4 trigger keys in v1.1.2 of km3net-Dataformat
trigger = self.keys.trigger
- keys = ['JTRIGGER3DSHOWER', 'JTRIGGERMXSHOWER',
- 'JTRIGGER3DMUON', 'JTRIGGERNB']
+ keys = [
+ 'JTRIGGER3DSHOWER', 'JTRIGGERMXSHOWER', 'JTRIGGER3DMUON',
+ 'JTRIGGERNB'
+ ]
values = [1, 2, 4, 5]
for k, v in zip(keys, values):
@@ -59,9 +61,10 @@ class TestOfflineKeys(unittest.TestCase):
def test_reconstruction(self):
# there are 34 parameters in v1.1.2 of km3net-Dataformat
reco = self.keys.reconstruction
- keys = ['JPP_RECONSTRUCTION_TYPE', 'JMUONFIT', 'JMUONBEGIN',
- 'JMUONPREFIT', 'JMUONSIMPLEX', 'JMUONGANDALF',
- 'JMUONENERGY', 'JMUONSTART']
+ keys = [
+ 'JPP_RECONSTRUCTION_TYPE', 'JMUONFIT', 'JMUONBEGIN', 'JMUONPREFIT',
+ 'JMUONSIMPLEX', 'JMUONGANDALF', 'JMUONENERGY', 'JMUONSTART'
+ ]
values = [4000, 0, 0, 1, 2, 3, 4, 5]
self.assertEqual(34, len([*reco.keys()]))
@@ -77,6 +80,7 @@ class TestOfflineKeys(unittest.TestCase):
for k, v in fit.items():
self.assertEqual(values[v], fit[k])
+
class TestReader(unittest.TestCase):
def setUp(self):
self.r = Reader(OFFLINE_FILE)
@@ -168,28 +172,27 @@ class TestOfflineReader(unittest.TestCase):
fitinf = self.nu.tracks.fitinf
rec_stages = self.nu.tracks.rec_stages
- empty_fitinf = np.array([match for match in
- self.nu._find_empty(fitinf)])
- empty_stages = np.array([match for match in
- self.nu._find_empty(rec_stages)])
+ empty_fitinf = np.array(
+ [match for match in self.nu._find_empty(fitinf)])
+ empty_stages = np.array(
+ [match for match in self.nu._find_empty(rec_stages)])
- self.assertListEqual(empty_fitinf[:5, 1].tolist(), [23, 14,
- 14, 4, None])
- self.assertListEqual(empty_stages[:5, 1].tolist(), [False, False,
- False, False,
- None])
+ self.assertListEqual(empty_fitinf[:5, 1].tolist(),
+ [23, 14, 14, 4, None])
+ self.assertListEqual(empty_stages[:5, 1].tolist(),
+ [False, False, False, False, None])
def test_find_rec_stages(self):
- stages = np.array([match for match in
- self.nu._find_rec_stages([1, 2, 3, 4, 5])])
+ stages = np.array(
+ [match for match in self.nu._find_rec_stages([1, 2, 3, 4, 5])])
self.assertListEqual(stages[:5, 1].tolist(), [0, 0, 0, 0, None])
def test_get_reco_fit(self):
- JGANDALF_BETA0_RAD = [0.0020367251782607574,
- 0.003306725805622178,
- 0.0057877124222254885,
- 0.015581698352185896]
+ JGANDALF_BETA0_RAD = [
+ 0.0020367251782607574, 0.003306725805622178, 0.0057877124222254885,
+ 0.015581698352185896
+ ]
reco_fit = self.nu.get_reco_fit([1, 2, 3, 4, 5])['JGANDALF_BETA0_RAD']
self.assertListEqual(JGANDALF_BETA0_RAD, reco_fit[:4].tolist())
@@ -201,18 +204,18 @@ class TestOfflineReader(unittest.TestCase):
max_reco = self.nu._get_max_reco_stages(rec_stages)
self.assertEqual(len(max_reco.tolist()), 9)
- self.assertListEqual(max_reco[0].tolist(), [[1, 2, 3, 4, 5],
- 5, 0])
+ self.assertListEqual(max_reco[0].tolist(), [[1, 2, 3, 4, 5], 5, 0])
def test_best_reco(self):
- JGANDALF_BETA1_RAD = [0.0014177681261476852,
- 0.002094094517471032,
- 0.003923368624980349,
- 0.009491461076780453]
+ JGANDALF_BETA1_RAD = [
+ 0.0014177681261476852, 0.002094094517471032, 0.003923368624980349,
+ 0.009491461076780453
+ ]
best = self.nu.best_reco
self.assertEqual(best.size, 9)
- self.assertEqual(best['JGANDALF_BETA1_RAD'][:4].tolist(), JGANDALF_BETA1_RAD)
+ self.assertEqual(best['JGANDALF_BETA1_RAD'][:4].tolist(),
+ JGANDALF_BETA1_RAD)
def test_reading_header(self):
# head is the supported format
@@ -407,16 +410,14 @@ class TestOfflineTracks(unittest.TestCase):
track_selection_2 = tracks[1:3]
assert 2 == len(track_selection_2)
for _slice in [
- slice(0, 0),
- slice(0, 1),
- slice(0, 2),
- slice(1, 5),
- slice(3, -2)
+ slice(0, 0),
+ slice(0, 1),
+ slice(0, 2),
+ slice(1, 5),
+ slice(3, -2)
]:
- self.assertListEqual(
- list(tracks.E[:,0][_slice]),
- list(tracks[_slice].E[:,0])
- )
+ self.assertListEqual(list(tracks.E[:, 0][_slice]),
+ list(tracks[_slice].E[:, 0]))
class TestOfflineTrack(unittest.TestCase):