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[feat] add autoformating
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6 files changed

+124
-46
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6 files changed

+124
-46
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‎autoformating.sh‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
autopep8 --verbose --in-place --aggressive --recursive ./fastanalysis

‎fastanalysis/load.py‎

Lines changed: 12 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,19 @@
11
import pandas
22
import os
33

4+
45
class Load:
56
"""Base class to load tracking.txt files"""
6-
7+
78
def __init__(self, path):
89
"""Constructor for the Load tracking object.
910
1011
:param path: Path to the tracking.txt file.
1112
:type path: str
12-
:raises Exception
13+
:raises Exception
1314
"""
1415
self.path = os.path.abspath(path)
15-
try:
16+
try:
1617
self.tracking = pandas.read_csv(path, sep='\t')
1718
except Exception as e:
1819
raise e
@@ -101,7 +102,8 @@ def getObjectsInFrames(self, ids, indexes):
101102
indexes = [indexes]
102103
if not isinstance(ids, list):
103104
ids = [ids]
104-
data = self.tracking[(self.tracking.imageNumber.isin(indexes))&(self.tracking.id.isin(ids))]
105+
data = self.tracking[(self.tracking.imageNumber.isin(
106+
indexes)) & (self.tracking.id.isin(ids))]
105107
return data
106108

107109
def isObjectsInFrame(self, ids, index):
@@ -117,20 +119,23 @@ def isObjectsInFrame(self, ids, index):
117119
isIn = []
118120
if isinstance(ids, list):
119121
for iD in ids:
120-
data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == iD)]
122+
data = self.tracking[(self.tracking.imageNumber == index) & (
123+
self.tracking.id == iD)]
121124
if data.empty:
122125
isIn.append(False)
123126
else:
124127
isIn.append(True)
125128
return isIn
126129
else:
127-
data = self.tracking[(self.tracking.imageNumber == index)&(self.tracking.id == ids)]
130+
data = self.tracking[(self.tracking.imageNumber == index) & (
131+
self.tracking.id == ids)]
128132
if data.empty:
129133
return False
130134
else:
131135
return True
132136

133-
def export(self, path, delimiter='\t', keys=None, ids=None, indexes=None, fmt="csv"):
137+
def export(self, path, delimiter='\t', keys=None,
138+
ids=None, indexes=None, fmt="csv"):
134139
"""Export the tracking data.
135140
136141
:param path: Path to the saved file.

‎fastanalysis/plot.py‎

Lines changed: 15 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
import matplotlib.pyplot as plt
44
import seaborn as sns
55

6+
67
class Plot:
78
"""Base class for plotting"""
89

@@ -14,7 +15,8 @@ def __init__(self, loadObject):
1415
"""
1516
self.data = loadObject.getDataframe()
1617

17-
def velocityDistribution(self, ids, indexes=None, key="Body", pooled=True, subplots=False):
18+
def velocityDistribution(self, ids, indexes=None,
19+
key="Body", pooled=True, subplots=False):
1820
"""Plot the velocity distribution.
1921
2022
:param ids: Ids of objects.
@@ -34,17 +36,23 @@ def velocityDistribution(self, ids, indexes=None, key="Body", pooled=True, subpl
3436
indexes = (0, len(self.data.imageNumber.values))
3537
if pooled:
3638
subplots = False
37-
tmpData = self.data[(self.data.id == ids[0])&(self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
38-
pooledData = (np.sqrt(np.diff(tmpData["x"+key].values)**2 + np.diff(tmpData["y"+key].values)**2)) / np.diff(tmpData.imageNumber.values)
39+
tmpData = self.data[(self.data.id == ids[0]) & (
40+
self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
41+
pooledData = (np.sqrt(np.diff(tmpData["x" + key].values)**2 + np.diff(
42+
tmpData["y" + key].values)**2)) / np.diff(tmpData.imageNumber.values)
3943
for i in ids[1::]:
40-
tmpData = self.data[(self.data.id == i)&(self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
41-
pooledData = np.concatenate((pooledData, (np.sqrt(np.diff(tmpData["x"+key].values)**2 + np.diff(tmpData["y"+key].values)**2)) / np.diff(tmpData.imageNumber.values)))
44+
tmpData = self.data[(self.data.id == i) & (
45+
self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
46+
pooledData = np.concatenate((pooledData, (np.sqrt(np.diff(
47+
tmpData["x" + key].values)**2 + np.diff(tmpData["y" + key].values)**2)) / np.diff(tmpData.imageNumber.values)))
4248
outputData = [pooledData]
4349
else:
4450
data = []
4551
for i in ids:
46-
tmpData = self.data[(self.data.id == i)&(self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
47-
data.append((np.sqrt(np.diff(tmpData["x"+key].values)**2 + np.diff(tmpData["y"+key].values)**2)) / np.diff(tmpData.imageNumber.values))
52+
tmpData = self.data[(self.data.id == i) & (
53+
self.data.imageNumber.isin(range(indexes[0], indexes[1])))]
54+
data.append((np.sqrt(np.diff(tmpData["x" + key].values)**2 + np.diff(
55+
tmpData["y" + key].values)**2)) / np.diff(tmpData.imageNumber.values))
4856
outputData = data
4957

5058
if subplots:

‎fastanalysis/tests/test_load.py‎

Lines changed: 70 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -3,57 +3,97 @@
33

44
import load
55

6+
67
def test_load_file():
78
"""Test that file is loaded as a dataframe."""
89
tracking = load.Load("tests/tracking.txt").getDataframe()
910
reference = pandas.read_csv("tests/tracking.txt", sep='\t')
1011
pandas.testing.assert_frame_equal(tracking, reference)
1112

13+
1214
def test_load_file_error():
1315
"""Test that wrong path lead to Exception."""
1416
with pytest.raises(Exception):
1517
tracking = load.Load("tests/tracing.txt").getDataframe()
1618
assert tracking
1719

20+
1821
def test_object_number():
1922
"""Test number of objects."""
2023
objectNumber = load.Load("tests/tracking.txt").getObjectNumber()
2124
assert objectNumber == 207
2225

26+
2327
def test_get_keys():
2428
"""Test get list of keys."""
2529
keys = load.Load("tests/tracking.txt").getKeys()
26-
assert keys == ["xHead", "yHead", "tHead", "xTail", "yTail", "tTail", "xBody", "yBody", "tBody", "curvature", "areaBody", "perimeterBody", "headMajorAxisLength", "headMinorAxisLength", "headExcentricity", "tailMajorAxisLength", "tailMinorAxisLength", "tailExcentricity", "bodyMajorAxisLength", "bodyMinorAxisLength", "bodyExcentricity", "imageNumber", "id"]
30+
assert keys == [
31+
"xHead",
32+
"yHead",
33+
"tHead",
34+
"xTail",
35+
"yTail",
36+
"tTail",
37+
"xBody",
38+
"yBody",
39+
"tBody",
40+
"curvature",
41+
"areaBody",
42+
"perimeterBody",
43+
"headMajorAxisLength",
44+
"headMinorAxisLength",
45+
"headExcentricity",
46+
"tailMajorAxisLength",
47+
"tailMinorAxisLength",
48+
"tailExcentricity",
49+
"bodyMajorAxisLength",
50+
"bodyMinorAxisLength",
51+
"bodyExcentricity",
52+
"imageNumber",
53+
"id"]
54+
2755

2856
def test_data_keys():
2957
"""Test get data from list of keys."""
3058
reference = pandas.read_csv("tests/tracking.txt", sep='\t')
31-
pandas.testing.assert_frame_equal(load.Load("tests/tracking.txt").getDataKeys(["yHead", "tHead"]), reference[["yHead", "tHead"]])
32-
pandas.testing.assert_frame_equal(load.Load("tests/tracking.txt").getDataKeys("yHead"), reference[["yHead"]])
59+
pandas.testing.assert_frame_equal(load.Load(
60+
"tests/tracking.txt").getDataKeys(["yHead", "tHead"]), reference[["yHead", "tHead"]])
61+
pandas.testing.assert_frame_equal(
62+
load.Load("tests/tracking.txt").getDataKeys("yHead"), reference[["yHead"]])
63+
3364

3465
def test_get_objects():
3566
"""Test get the data for an object"""
3667
reference = pandas.read_csv("tests/tracking.txt", sep='\t')
3768
tracking = load.Load("tests/tracking.txt").getObjects(0)
38-
pandas.testing.assert_frame_equal(tracking, reference[reference.id==0])
69+
pandas.testing.assert_frame_equal(tracking, reference[reference.id == 0])
3970
tracking = load.Load("tests/tracking.txt").getObjects([0, 1])
40-
pandas.testing.assert_frame_equal(tracking, reference[(reference.id==1)|(reference.id==0)])
41-
71+
pandas.testing.assert_frame_equal(
72+
tracking, reference[(reference.id == 1) | (reference.id == 0)])
73+
74+
4275
def test_get_frames():
4376
"""Test get the data for a frame"""
4477
reference = pandas.read_csv("tests/tracking.txt", sep='\t')
4578
tracking = load.Load("tests/tracking.txt").getFrames(10)
46-
pandas.testing.assert_frame_equal(tracking, reference[reference.imageNumber==10])
79+
pandas.testing.assert_frame_equal(
80+
tracking, reference[reference.imageNumber == 10])
4781
tracking = load.Load("tests/tracking.txt").getFrames([1, 10])
48-
pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==1)|(reference.imageNumber==10)])
82+
pandas.testing.assert_frame_equal(tracking, reference[(
83+
reference.imageNumber == 1) | (reference.imageNumber == 10)])
84+
4985

5086
def test_get_objects_in_frames():
5187
"""Test get the data for an frame"""
5288
reference = pandas.read_csv("tests/tracking.txt", sep='\t')
5389
tracking = load.Load("tests/tracking.txt").getObjectsInFrames(0, 200)
54-
pandas.testing.assert_frame_equal(tracking, reference[(reference.imageNumber==200)&(reference.id==0)])
55-
tracking = load.Load("tests/tracking.txt").getObjectsInFrames([1, 2], [0, 100])
56-
pandas.testing.assert_frame_equal(tracking, reference[((reference.imageNumber==100)|(reference.imageNumber==0))&((reference.id==1)|(reference.id==2))])
90+
pandas.testing.assert_frame_equal(tracking, reference[(
91+
reference.imageNumber == 200) & (reference.id == 0)])
92+
tracking = load.Load(
93+
"tests/tracking.txt").getObjectsInFrames([1, 2], [0, 100])
94+
pandas.testing.assert_frame_equal(tracking, reference[((reference.imageNumber == 100) | (
95+
reference.imageNumber == 0)) & ((reference.id == 1) | (reference.id == 2))])
96+
5797

5898
def test_is_objects_in_frame():
5999
"""Test check if objects in frame"""
@@ -63,6 +103,7 @@ def test_is_objects_in_frame():
63103
tracking = load.Load("tests/tracking.txt").isObjectsInFrame(0, 1500)
64104
assert not tracking
65105

106+
66107
def test_export_csv():
67108
"""Test set the data in a file"""
68109
reference = pandas.read_csv("tests/tracking.txt", sep='\t')
@@ -75,22 +116,26 @@ def test_export_csv():
75116
tracking.export("tests/test.csv", delimiter=',')
76117
test = pandas.read_csv("tests/test.csv", sep=',')
77118
pandas.testing.assert_frame_equal(reference, test)
78-
119+
79120
tracking.export("tests/test.csv", keys=["imageNumber"])
80121
test = pandas.read_csv("tests/test.csv", sep='\t')
81122
pandas.testing.assert_frame_equal(reference[["imageNumber"]], test)
82-
123+
83124
tracking.export("tests/test.csv", indexes=[1])
84125
test = pandas.read_csv("tests/test.csv", sep='\t')
85-
pandas.testing.assert_frame_equal(reference[reference.imageNumber==1].reset_index(drop=True), test)
126+
pandas.testing.assert_frame_equal(
127+
reference[reference.imageNumber == 1].reset_index(drop=True), test)
86128

87129
tracking.export("tests/test.csv", ids=[0])
88130
test = pandas.read_csv("tests/test.csv", sep='\t')
89-
pandas.testing.assert_frame_equal(reference[reference.id==0].reset_index(drop=True), test)
90-
131+
pandas.testing.assert_frame_equal(
132+
reference[reference.id == 0].reset_index(drop=True), test)
133+
91134
tracking.export("tests/test.csv", ids=[0], indexes=[0])
92135
test = pandas.read_csv("tests/test.csv", sep='\t')
93-
pandas.testing.assert_frame_equal(reference[(reference.id==0) & (reference.imageNumber==0)].reset_index(drop=True), test)
136+
pandas.testing.assert_frame_equal(reference[(reference.id == 0) & (
137+
reference.imageNumber == 0)].reset_index(drop=True), test)
138+
94139

95140
def test_export_excel():
96141
"""Test set the data in an excel file"""
@@ -104,15 +149,18 @@ def test_export_excel():
104149
tracking.export("tests/test.xlsx", keys=["imageNumber"], fmt="excel")
105150
test = pandas.read_excel("tests/test.xlsx")
106151
pandas.testing.assert_frame_equal(reference[["imageNumber"]], test)
107-
152+
108153
tracking.export("tests/test.xlsx", indexes=[1], fmt="excel")
109154
test = pandas.read_excel("tests/test.xlsx")
110-
pandas.testing.assert_frame_equal(reference[reference.imageNumber==1].reset_index(drop=True), test)
155+
pandas.testing.assert_frame_equal(
156+
reference[reference.imageNumber == 1].reset_index(drop=True), test)
111157

112158
tracking.export("tests/test.xlsx", ids=[0], fmt="excel")
113159
test = pandas.read_excel("tests/test.xlsx")
114-
pandas.testing.assert_frame_equal(reference[reference.id==0].reset_index(drop=True), test)
115-
160+
pandas.testing.assert_frame_equal(
161+
reference[reference.id == 0].reset_index(drop=True), test)
162+
116163
tracking.export("tests/test.xlsx", ids=[0], indexes=[0], fmt="excel")
117164
test = pandas.read_excel("tests/test.xlsx")
118-
pandas.testing.assert_frame_equal(reference[(reference.id==0) & (reference.imageNumber==0)].reset_index(drop=True), test)
165+
pandas.testing.assert_frame_equal(reference[(reference.id == 0) & (
166+
reference.imageNumber == 0)].reset_index(drop=True), test)

‎fastanalysis/tests/test_plot.py‎

Lines changed: 19 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -12,9 +12,11 @@ def test_velocity_dist_default_key():
1212
plotObj = plot.Plot(tracking)
1313
velocityTest = plotObj.velocityDistribution(ids=[0, 1])
1414
refData = tracking.getObjects(0)
15-
a = (np.sqrt(np.diff(refData.xBody.values)**2 + np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
15+
a = (np.sqrt(np.diff(refData.xBody.values)**2 +
16+
np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
1617
refData = tracking.getObjects(1)
17-
b = (np.sqrt(np.diff(refData.xBody.values)**2 + np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
18+
b = (np.sqrt(np.diff(refData.xBody.values)**2 +
19+
np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
1820
pooled = np.concatenate((a, b))
1921
np.testing.assert_array_equal(pooled, velocityTest[1][0])
2022

@@ -23,27 +25,35 @@ def test_velocity_dist_default_key():
2325
np.testing.assert_array_equal(b, velocityTest[1][1])
2426

2527
refData = tracking.getObjectsInFrames(0, indexes=list(range(0, 100)))
26-
a = (np.sqrt(np.diff(refData.xBody.values)**2 + np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
27-
velocityTest = plotObj.velocityDistribution(ids=[0], pooled=True, indexes=(0, 100))
28+
a = (np.sqrt(np.diff(refData.xBody.values)**2 +
29+
np.diff(refData.yBody.values)**2)) / np.diff(refData.imageNumber.values)
30+
velocityTest = plotObj.velocityDistribution(
31+
ids=[0], pooled=True, indexes=(0, 100))
2832
np.testing.assert_array_equal(a, velocityTest[1][0])
2933

34+
3035
def test_velocity_dist_head():
3136
"""Test velocity distribution."""
3237
tracking = load.Load("tests/tracking.txt")
3338
plotObj = plot.Plot(tracking)
3439
velocityTest = plotObj.velocityDistribution(ids=[0, 1], key="Head")
3540
refData = tracking.getObjects(0)
36-
a = (np.sqrt(np.diff(refData.xHead.values)**2 + np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
41+
a = (np.sqrt(np.diff(refData.xHead.values)**2 +
42+
np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
3743
refData = tracking.getObjects(1)
38-
b = (np.sqrt(np.diff(refData.xHead.values)**2 + np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
44+
b = (np.sqrt(np.diff(refData.xHead.values)**2 +
45+
np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
3946
pooled = np.concatenate((a, b))
4047
np.testing.assert_array_equal(pooled, velocityTest[1][0])
4148

42-
velocityTest = plotObj.velocityDistribution(ids=[0, 1], pooled=False, key="Head")
49+
velocityTest = plotObj.velocityDistribution(
50+
ids=[0, 1], pooled=False, key="Head")
4351
np.testing.assert_array_equal(a, velocityTest[1][0])
4452
np.testing.assert_array_equal(b, velocityTest[1][1])
4553

4654
refData = tracking.getObjectsInFrames(0, indexes=list(range(0, 100)))
47-
a = (np.sqrt(np.diff(refData.xHead.values)**2 + np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
48-
velocityTest = plotObj.velocityDistribution(ids=[0], pooled=True, indexes=(0, 100), key="Head")
55+
a = (np.sqrt(np.diff(refData.xHead.values)**2 +
56+
np.diff(refData.yHead.values)**2)) / np.diff(refData.imageNumber.values)
57+
velocityTest = plotObj.velocityDistribution(
58+
ids=[0], pooled=True, indexes=(0, 100), key="Head")
4959
np.testing.assert_array_equal(a, velocityTest[1][0])

‎setup.py‎

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,13 @@
88
description="A python library to open the tracking data from FastTrack the tracking software",
99
url="https://github.com/FastTrackOrg/FastAnalysis",
1010
packages=['fastanalysis'],
11-
install_requires=['pandas', 'numpy', 'matplotlib', 'xlrd', 'openpyxl', 'seaborn'],
11+
install_requires=[
12+
'pandas',
13+
'numpy',
14+
'matplotlib',
15+
'xlrd',
16+
'openpyxl',
17+
'seaborn'],
1218
license='MIT',
1319
python_requires='>=3.6',
1420
zip_safe=False

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