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ijmpy_unit_tests.py
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ijmpy_unit_tests.py
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from __future__ import print_function, division
import __builtin__
import sys, time, unittest, math, os
from ij import WindowManager
from ij.gui import Roi
from ij.macro import Interpreter
from mripy.ijmpy import *
class MathTest(unittest.TestCase):
def testAcos(self):
value = acos(0.5)
self.assertEquals(round(value, 3), 1.047)
def testAsin(self):
value = asin(0.5)
self.assertEquals(round(value, 3), 0.524)
def testAtan(self):
value = atan(0.5)
self.assertEquals(round(value, 3), 0.464)
def testAtan2(self):
value = atan2(2, 1)
self.assertEquals(round(value,4), 1.1071)
def testCos(self):
res = cos(2*PI)
self.assertEquals(res, 1)
def testExp(self):
res1 = exp(1)
res2 = exp(2)
self.assertEquals(res1, math.e)
self.assertEquals(round(res2, 14), round(math.e**2, 14))
def testFloor(self):
res = floor(3.78)
self.assertEquals(res, 3)
class ArrayTest(unittest.TestCase):
def testConcat(self):
array1 = newArray(1, 2, 3)
array2 = newArray("a", "b")
element1 = "c"
element2 = 4
array = Array.concat(element1, array1)
self.assertEquals(len(array), 4)
self.assertEquals(array[0], "c")
self.assertEquals(array[1], 1)
array = Array.concat(array, element2)
self.assertEquals(len(array), 5)
self.assertEquals(array[-1], 4)
self.assertEquals(array[-2], 3)
array = Array.concat(array, array2)
self.assertEquals(len(array), 7)
self.assertEquals(array[-1], "b")
self.assertEquals(array[0], "c")
def testCopy(self):
array = newArray(1, 2, 3, 4)
copyOfArray = Array.copy(array)
copyOfArray[1] = 2.5
self.assertEquals(copyOfArray[0], 1)
self.assertEquals(copyOfArray[1], 2.5)
self.assertEquals(copyOfArray[2], 3)
self.assertEquals(copyOfArray[3], 4)
self.assertEquals(array[1], 2)
def testDeleteValue(self):
array = newArray(1,0,2,3,0,0,4,0,5,0,0,6,0,0,0,7)
array = Array.deleteValue(array, 0)
self.assertEquals(len(array), 7)
def testDeleteIndex(self):
array = [1, 2, 3, 4]
res1 = Array.deleteIndex(array, 0)
res2 = Array.deleteIndex(array, 1)
res3 = Array.deleteIndex(array, 2)
res4 = Array.deleteIndex(array, 3)
self.assertEquals(len(res1), 3)
self.assertEquals(res1[0], 2)
self.assertEquals(len(res2), 3)
self.assertEquals(res2[1], 3)
self.assertEquals(len(res3), 3)
self.assertEquals(res3[2], 4)
self.assertEquals(len(res4), 3)
self.assertEquals(res4[2], 3)
def testFill(self):
array = [1, 2, 3, 4]
Array.fill(array, 5)
self.assertEquals(len(array), 4)
self.assertEquals(array[0], 5)
self.assertEquals(array[1], 5)
self.assertEquals(array[2], 5)
self.assertEquals(array[3], 5)
def testFindMaxima(self):
array = [1, 2, 3, 4, 5, 4, 3, 2, 3, 4, 5, 6, 7, 8, 7, 6, 6, 5]
maxima = Array.findMaxima(array, 1)
self.assertEquals(maxima[0], 13)
self.assertEquals(maxima[1], 4)
def testFindMinima(self):
array = [10, 9, 8, 7, 6, 7, 8, 9, 10, 10, 9, 8, 7, 6, 7, 8, 9, 9]
minima = Array.findMinima(array, 1)
self.assertEquals(minima[0], 13)
self.assertEquals(minima[1], 4)
def testFourier(self):
array = [0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1]
fourier = Array.fourier(array)
self.assertEquals(fourier[0], 0.25)
self.assertEquals(round(fourier[8],4), 0.3536)
def testGetSequence(self):
seq = Array.getSequence(4)
self.assertEquals(len(seq), 4)
self.assertEquals(seq[0], 0)
self.assertEquals(seq[1], 1)
self.assertEquals(seq[2], 2)
self.assertEquals(seq[3], 3)
def testGetStatistics(self):
array = [1, 2, 3, 4, 5, 6, 7 ,8, 9, 10]
min, max, mean, stddev = Array.getStatistics(array)
self.assertEquals(min, 1)
self.assertEquals(max, 10)
self.assertEquals(mean, 5.5)
self.assertEquals(round(stddev, 4), 3.0277)
def testPrint(self):
array = [1, 2, 3, 'a', 'b']
Array.print(array)
content = IJ.getLog()
lines = content.split("\n")
self.assertEquals(lines[-2], "1, 2, 3, a, b")
def testRankPositionsInt(self):
array = [10, 9, 8, 7, 7, 6 ,5]
ranks = Array.rankPositions(array)
self.assertEquals(ranks[0], 6)
self.assertEquals(ranks[1], 5)
self.assertEquals(ranks[2], 3)
self.assertEquals(ranks[3], 4)
self.assertEquals(ranks[4], 2)
self.assertEquals(ranks[5], 1)
self.assertEquals(ranks[6], 0)
def testRankPositionsString(self):
array = ["the", "quick", "brown", "fox"]
ranks = Array.rankPositions(array)
self.assertEquals(ranks[0], 2)
self.assertEquals(ranks[1], 3)
self.assertEquals(ranks[2], 1)
self.assertEquals(ranks[3], 0)
def testResampleBigger(self):
array = [1, 2, 3, 4, 5]
resampled = Array.resample(array, 10)
self.assertEquals(len(resampled), 10)
self.assertEquals(resampled[0], 1)
self.assertEquals(resampled[-1], 5)
def testResampleSmaller(self):
array = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
resampled = Array.resample(array, 5)
self.assertEquals(len(resampled), 5)
self.assertEquals(resampled[0], 1)
self.assertEquals(resampled[-1], 10)
def testReverse(self):
array = [1, 2, 3]
Array.reverse(array)
self.assertEquals(array[0], 3)
self.assertEquals(array[1], 2)
self.assertEquals(array[2], 1)
def testShowOneArray(self):
array = [1.234, 2.345, 3.456, 4.567]
rt = Array.show(array);
run('Close')
self.assertEquals(rt.getTitle(), "array")
self.assertEquals(rt.getColumnHeading(0), "Value")
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
def testShowTwoArrays(self):
array1 = [1.234, 2.345, 3.456, 4.567]
array2 = [5.678, 6.789, 7.890, 8.901]
rt = Array.show(array1, array2);
run('Close')
self.assertEquals(rt.getTitle(), "Arrays")
self.assertEquals(rt.getColumnHeading(0), "array1")
self.assertEquals(rt.getColumnHeading(1), "array2")
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
values = rt.getColumn(1)
self.assertEquals(round(values[0], 3), 5.678)
self.assertEquals(round(values[1], 3), 6.789)
self.assertEquals(round(values[2], 3), 7.890)
self.assertEquals(round(values[3], 3), 8.901)
def testShowArrayWithTitle(self):
array = [1.234, 2.345, 3.456, 4.567]
rt = Array.show('data', array);
run('Close')
self.assertEquals(rt.getTitle(), "data")
self.assertEquals(rt.getColumnHeading(0), "Value")
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
def testShowTwoArraysWithTitle(self):
array1 = [1.234, 2.345, 3.456, 4.567]
array2 = [5.678, 6.789, 7.890, 8.901]
rt = Array.show('data', array1, array2);
run('Close')
self.assertEquals(rt.getTitle(), "data")
self.assertEquals(rt.getColumnHeading(0), "array1")
self.assertEquals(rt.getColumnHeading(1), "array2")
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
values = rt.getColumn(1)
self.assertEquals(round(values[0], 3), 5.678)
self.assertEquals(round(values[1], 3), 6.789)
self.assertEquals(round(values[2], 3), 7.890)
self.assertEquals(round(values[3], 3), 8.901)
def testShowTwoArraysWithIndexes(self):
array1 = [1.234, 2.345, 3.456, 4.567]
array2 = [5.678, 6.789, 7.890, 8.901]
rt = Array.show('data (indexes)', array1, array2);
run('Close')
self.assertEquals(rt.getTitle(), "data")
self.assertEquals(rt.getColumnHeading(0), "array1")
self.assertEquals(rt.getColumnHeading(1), "array2")
row = rt.getRowAsString(0)
columns = row.split("\t")
self.assertEquals(columns[0], '0')
row = rt.getRowAsString(3)
columns = row.split("\t")
self.assertEquals(columns[0], '3')
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
values = rt.getColumn(1)
self.assertEquals(round(values[0], 3), 5.678)
self.assertEquals(round(values[1], 3), 6.789)
self.assertEquals(round(values[2], 3), 7.890)
self.assertEquals(round(values[3], 3), 8.901)
def testShowTwoArraysWithRowNumbers(self):
array1 = [1.234, 2.345, 3.456, 4.567]
array2 = [5.678, 6.789, 7.890, 8.901]
rt = Array.show('data (row numbers)', array1, array2);
run('Close')
self.assertEquals(rt.getTitle(), "data")
self.assertEquals(rt.getColumnHeading(0), "array1")
self.assertEquals(rt.getColumnHeading(1), "array2")
row = rt.getRowAsString(0)
columns = row.split("\t")
self.assertEquals(columns[0], '1')
row = rt.getRowAsString(3)
columns = row.split("\t")
self.assertEquals(columns[0], '4')
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
values = rt.getColumn(1)
self.assertEquals(round(values[0], 3), 5.678)
self.assertEquals(round(values[1], 3), 6.789)
self.assertEquals(round(values[2], 3), 7.890)
self.assertEquals(round(values[3], 3), 8.901)
def testShowArrayResults(self):
close('Results')
array = [1.234, 2.345, 3.456, 4.567]
rt = Array.show('Results', array);
self.assertEquals(rt.getTitle(), "Results")
self.assertEquals(rt.getColumnHeading(0), "Value")
values = rt.getColumn(0)
self.assertEquals(round(values[0], 3), 1.234)
self.assertEquals(round(values[1], 3), 2.345)
self.assertEquals(round(values[2], 3), 3.456)
self.assertEquals(round(values[3], 3), 4.567)
close('Results')
def testSlice(self):
array = [1, 2, 3, 4, 5]
# remove first element
sliced = Array.slice(array, 1)
self.assertEquals(sliced[0], 2)
# remove last element
sliced = Array.slice(array, 0, len(array)-1);
self.assertEquals(sliced[-1], 4)
# extract first two elements
sliced = Array.slice(array, 0, 2)
self.assertEquals(sliced[0], 1)
self.assertEquals(sliced[1], 2)
self.assertEquals(len(sliced), 2)
# extract last two elements
sliced = Array.slice(array, len(array)-2);
self.assertEquals(sliced[0], 4)
self.assertEquals(sliced[1], 5)
self.assertEquals(len(sliced), 2)
def testSort(self):
array = ["delta", "alpha", "Gamma", "Beta"]
Array.sort(array)
self.assertEquals(array[0], 'alpha')
self.assertEquals(array[1], 'Beta')
self.assertEquals(array[2], 'delta')
self.assertEquals(array[3], 'Gamma')
array = [4, 2, 3, 1]
Array.sort(array)
self.assertEquals(array[0], 1)
self.assertEquals(array[1], 2)
self.assertEquals(array[2], 3)
self.assertEquals(array[3], 4)
def testTrim(self):
array = [1, 2, 3, 4, 5, 6, 7, 8]
trimmed = Array.trim(array, 3)
self.assertEquals(len(trimmed), 3)
self.assertEquals(trimmed[0], 1)
self.assertEquals(trimmed[1], 2)
self.assertEquals(trimmed[2], 3)
array = [1, 2, 3]
trimmed = Array.trim(array, 5)
self.assertEquals(len(trimmed), 3)
self.assertEquals(trimmed[0], 1)
self.assertEquals(trimmed[1], 2)
self.assertEquals(trimmed[2], 3)
def testRotate(self):
array = [0, 1, 2, "three", 4, 5, 6, 7, 8, 9]
Array.rotate(array, 1)
self.assertEquals(len(array), 10)
self.assertEquals(array[0], 9)
self.assertEquals(array[-1], 8)
array = [0, 1, 2, "three", 4, 5, 6, 7, 8, 9]
Array.rotate(array, -3)
self.assertEquals(len(array), 10)
self.assertEquals(array[0], 'three')
self.assertEquals(array[-1], 2)
def testGetVertexAngles(self):
x = [260.0004, 242.7981, 197.8065, 142.1838, 97.1959, 79.9999, 97.2080, 142.2034, 197.8261, 242.8102]
y = [170, 222.8958, 255.6012, 255.5979, 222.8874, 169.9895, 117.0956, 84.3954, 84.4054, 117.1212]
angles = Array.getVertexAngles(x, y, 1)
self.assertEquals(len(angles), 10)
self.assertEquals(round(angles[0]), 36.0)
self.assertEquals(round(angles[9]), 36.0)
class CallTest(unittest.TestCase):
def testNoParameter(self):
ver = call('ij.IJ.getVersion')
containsPoint = (ver.find('.') >=0)
containsSlash = (ver.find('/') >=0)
self.assertEquals(containsPoint, True)
self.assertEquals(containsSlash, True)
def testWithParameter(self):
demoString = call("ij.Prefs.get", "demo.string", "Text for preferences file")
self.assertEquals(demoString, "Text for preferences file")
class CloseTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testCloseNoParameter(self):
newImage("Ramp", "8-bit ramp", 256, 256, 1);
self.assertEqual(nImages(), 1);
close();
self.assertEqual(nImages(), 0)
def testCloseWithParameter(self):
newImage("Ramp", "8-bit ramp", 256, 256, 1);
newImage("Ramp2", "8-bit ramp", 256, 256, 1);
self.assertEqual(nImages(), 2);
close("*");
self.assertEqual(nImages(), 0)
class AutoUpdateTest(unittest.TestCase):
def testAutoUpdate(self):
autoUpdate(False)
self.assertEquals(isAutoUpdate(), False)
autoUpdate(True)
self.assertEquals(isAutoUpdate(), True)
class BeepTest(unittest.TestCase):
def testBeep(self):
beep()
self.assertEquals(True, True)
class BitDepthTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testBitDepth8(self):
newImage("Ramp", "8-bit ramp", 256, 256, 1);
bd = bitDepth()
self.assertEquals(bd, 8)
def testBitDepth16(self):
newImage("Ramp", "16-bit ramp", 256, 256, 1);
bd = bitDepth()
self.assertEquals(bd, 16)
def testBitDepth24(self):
newImage("Ramp", "RGB ramp", 256, 256, 1);
bd = bitDepth()
self.assertEquals(bd, 24)
def testBitDepth32(self):
newImage("Ramp", "32-bit ramp", 256, 256, 1);
bd = bitDepth()
self.assertEquals(bd, 32)
class CalibrateTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testCalibrateNone(self):
newImage("Ramp", "8-bit ramp", 256, 256, 1);
cv = calibrate(128)
self.assertEquals(cv, 128)
def testCalibrate(self):
imp = newImage("Ramp", "8-bit ramp", 256, 256, 1);
IJ.run(imp, "Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0 255] text2=[0 1]");
cv = calibrate(0)
self.assertEquals(cv, 0)
cv = calibrate(255)
self.assertEquals(cv, 1)
class ChangeValuesTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def test8BitWithoutRoi(self):
imp = newImage("Ramp", "8-bit ramp", 256, 256, 1);
changeValues(100, 110, 255);
self.assertEquals(getPixel(99, 0), 99)
self.assertEquals(getPixel(100, 0), 255)
self.assertEquals(getPixel(110, 0), 255)
self.assertEquals(getPixel(111, 0), 111)
def test8BitWithRoi(self):
imp = newImage("Ramp", "8-bit ramp", 256, 256, 1);
IJ.makeRectangle(10, 10, 10, 10)
changeValues(0, 100, 255);
self.assertEquals(getPixel(9, 15), 9)
self.assertEquals(getPixel(10, 15), 255)
self.assertEquals(getPixel(19, 15), 255)
self.assertEquals(getPixel(20, 15), 20)
def test16Bit(self):
imp = newImage("Ramp", "16-bit ramp", 256, 256, 1);
changeValues(100*256, 110*256, 255);
self.assertEquals(getPixel(99, 0), 99*256)
self.assertEquals(getPixel(100, 0), 255)
self.assertEquals(getPixel(110, 0), 255)
self.assertEquals(getPixel(111, 0), 111*256)
def test32Bit(self):
imp = newImage("Ramp", "32-bit ramp", 256, 256, 1);
changeValues(100/256.0, 110/256.0, 1);
self.assertEquals(getPixel(99, 0), 99/256.0)
self.assertEquals(getPixel(100, 0), 1)
self.assertEquals(getPixel(110, 0), 1)
self.assertEquals(getPixel(111, 0), 111/256.0)
class CharCodeAtTest(unittest.TestCase):
def testCharCodeAt(self):
name = 'Bäcker'
code = charCodeAt(name, 1)
self.assertEquals(code, 228)
class D2STest(unittest.TestCase):
def testD2S(self):
res = d2s(2/3.0, 2)
self.assertEquals(res, '0.67')
class DoCommandTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testDoCommand(self):
newImage("HyperStack", "8-bit composite-mode label", 400, 400, 1, 1, 20);
doCommand("Start Animation");
scriptIsStillRunning = True
self.assertEquals(scriptIsStillRunning, True)
class DoWandTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testDoWand(self):
imp = newImage("test", "8-bit black", 256, 256, 1);
IJ.makeRectangle(10, 10, 100, 100)
IJ.setForegroundColor(255, 255, 255);
run("Fill", "slice");
run("Select None");
doWand(50, 50);
roi = IJ.getImage().getRoi()
self.assertEquals(len(roi.getContainedPoints()), 10000)
class DrawTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
imp = newImage("test", "8-bit black", 256, 256, 1);
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testDrawLine(self):
IJ.setForegroundColor(255, 255, 255)
drawLine(10, 10, 100, 100);
v1 = getPixel(9, 9);
v2 = getPixel(10, 10);
v3 = getPixel(50, 50);
v4 = getPixel(100, 100);
v5 = getPixel(101, 101);
self.assertEquals(v1, 0)
self.assertEquals(v2, 255)
self.assertEquals(v3, 255)
self.assertEquals(v4, 255)
self.assertEquals(v5, 0)
def testDrawOval(self):
IJ.setForegroundColor(255, 255, 255)
drawOval(128, 128, 50, 50);
roi = doWand(150, 150)
self.assertEquals(len(roi.getContainedPoints()), 1877)
def testDrawRect(self):
IJ.setForegroundColor(255, 255, 255)
drawRect(128, 128, 50, 50);
roi = doWand(150, 150)
self.assertEquals(len(roi.getContainedPoints()), 2304)
def testDrawString(self):
IJ.setForegroundColor(255, 255, 255)
drawString("The quick brown fox...", 50, 50);
roi = doWand(54, 38);
self.assertEquals(len(roi.getContainedPoints()), 15)
class EndsWithTest(unittest.TestCase):
def testEndsWith(self):
self.assertEquals(endsWith('ijmpy.py','py'), True)
self.assertEquals(endsWith('ijmpy.py','ijm'), False)
class EvalTest(unittest.TestCase):
def testEvalScript(self):
resText = eval("script", '"ijmpy".bold();')
self.assertEquals(resText, '<b>ijmpy</b>');
def testEvalJS(self):
resText = eval("js", '"ijmpy".blink();')
self.assertEquals(resText, '<blink>ijmpy</blink>');
def testEvalBsh(self):
resText = eval("bsh", '2 + 2;')
self.assertEquals(resText, '4');
def testEvalPython(self):
resText = eval('python', 'import ij\nij.IJ.log("py")')
log = IJ.getLog()
log = log.split('\n')
self.assertEquals(log[-2], "py")
def testEvalMacro(self):
resText = eval('sqrt(getArgument())', '9')
log = IJ.getLog()
log = log.split('\n')
self.assertEquals(log[-2], "3")
class ExecTest(unittest.TestCase):
def testExec(self):
out = Exec('echo', 'hi echo')
self.assertEquals(out, 'hi echo\n')
class ExtTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testExt(self):
IJ.run("New Image5D", "name=Untitled type=8-bit fill=Ramp width=256 height=256 channels=3 slices=1 frames=1");
Ext.install('sc.fiji.i5d.plugin.Image5D_Extensions')
Ext.setDisplayMode('overlay')
dm = Ext.getDisplayMode()
self.assertEquals(dm, 'overlay')
Ext.setDisplayMode('color')
dm = Ext.getDisplayMode()
self.assertEquals(dm, 'color')
class FileTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
if os.path.exists('./test.txt'):
os.remove('./test.txt')
if os.path.exists('./test'):
os.rmdir('./test')
def tearDown(self):
unittest.TestCase.tearDown(self)
if os.path.exists('./test.txt'):
os.remove('./test.txt')
if os.path.exists('./test'):
os.rmdir('./test')
def testAppend(self):
File.append('THE END', './test.txt')
with open('./test.txt', 'r') as aFile:
content = aFile.read()
lines = content.split('\n')
self.assertEquals(lines[-1], 'THE END')
def testOpen(self):
aFile = File.open('./test.txt')
print(aFile, 'test test')
File.close(aFile)
with open ("/home/baecker/test.txt", "r") as myfile:
data=myfile.readlines()[0]
self.assertEquals(data, 'test test')
def testClose(self):
aFile = File.open('./test.txt')
print(aFile, 'test test')
File.close(aFile)
self.assertEquals(aFile.closed, True)
def testCopy(self):
aFile = File.open('./test.txt')
print(aFile, 'test test')
File.close(aFile)
File.copy('./test.txt', './test2.txt')
with open ("./test2.txt", "r") as myfile:
data=myfile.readlines()[0]
self.assertEquals(data, 'test test')
os.remove('./test2.txt')
def testDateLastModified(self):
before = time.ctime()
f = File.open('test.txt')
print(f, "test test")
File.close(f)
mtime = time.ctime(os.path.getmtime("test.txt"))
after = time.ctime()
self.assertEquals(before<=mtime, True)
self.assertEquals(mtime<=after, True)
def testDelete(self):
f = File.open('test.txt')
print(f, "test test")
File.close(f)
self.assertEquals(os.path.isfile('test.txt'), True)
File.delete('test.txt')
self.assertEquals(os.path.isfile('test.txt'), False)
def testDirectory(self):
aDir = File.directory
self.assertEquals(os.path.isdir(aDir) or aDir=='', True)
def testGetDefaultDir(self):
cDir = File.getDefaultDir()
self.assertEquals(os.path.isdir(cDir), True)
def testSetDefaultDir(self):
dd = File.getDefaultDir()
os.mkdir('./ijmpytest')
File.setDefaultDir('./ijmpytest')
self.assertEquals(File.getDefaultDir(), dd + '/ijmpytest')
File.setDefaultDir(dd)
File.delete('./ijmpytest')
def testExists(self):
res = File.exists('.')
self.assertEquals(res, True)
res = File.exists('/mumpitz')
self.assertEquals(res, False)
f = File.open('test.txt')
print(f, "test test")
File.close(f)
res = File.exists('test.txt')
self.assertEquals(res, True)
def testGetName(self):
name = File.getName('a/b/c/blobs.tif')
self.assertEquals(name, 'blobs.tif')
def testGetNameWithoutExtension(self):
name = File.getNameWithoutExtension('a/b/c/blobs.tif')
self.assertEquals(name, 'blobs')
def testGetDirectory(self):
aDir = File.getDirectory('a/b/c/blobs.tif')
self.assertEquals(aDir, 'a/b/c')
def testGetParent(self):
parent = File.getParent('/a/b/c')
self.assertEquals(parent, '/a/b')
def testIsDirectory(self):
self.assertEquals(File.isDirectory("./"), True)
self.assertEquals(File.isDirectory("./test.txt"), False)
def testLastModified(self):
before = round(time.time(), 0) - 1
f = File.open('test.txt')
print(f, "test test")
File.close(f)
lastModified = File.lastModified('./test.txt')
after = time.time()
print(before, lastModified, after)
self.assertEquals(before<=lastModified, True)
self.assertEquals(lastModified<=after, True)
def testLength(self):
f = File.open('test.txt')
print(f, "test test")
File.close(f)
l = File.length('test.txt')
self.assertEquals(l, 9)
def testMakeDirectory(self):
File.makeDirectory('test')
self.assertEquals(File.isDirectory('test'), True)
File.delete('test')
def testName(self):
aName = File.name
aDir = File.directory
self.assertEquals(os.path.isfile(aDir+'/'+aName) or aName=='' or aDir=='', True)
def testNameWithoutExtension(self):
aNameWithExt = File.name
aNameWithoutExt = File.nameWithoutExtension
n = len(aNameWithExt.split('.')) - len(aNameWithoutExt.split('.'))
self.assertEquals(aNameWithExt=='' or (n>=0 and n<2), True)
def testOpenAsString(self):
f = File.open('test.txt')
print(f, "test test")
File.close(f)
text = File.openAsString('test.txt')
self.assertEquals(text, "test test\n")
def testOpenAsRawString(self):
iconPath = IJ.getDirectory('imagej') + 'images/icon.png'
out = File.openAsRawString(iconPath)
self.assertEquals(len(out), 5000)
def testOpenUrlAsString(self):
content = File.openUrlAsString('https://imagej.net/developer/macro/functions.html')
self.assertEquals(content.split('\n')[0].startswith('<!DOCTYPE'), True)
content = File.openUrlAsString('malformed')
self.assertEquals(content.split('\n')[0].startswith('<Error'), True)
content = File.openUrlAsString('https://gibtsnicht')
self.assertEquals(content.split('\n')[0].startswith('<Error'), True)
def testRename(self):
f = File.open('test.txt')
print(f, "test test")
File.close(f)
res = File.rename('test.txt', 'test2.txt')
self.assertEquals(res, True)
res = File.rename('test2.txt', 'test.txt')
def testSaveString(self):
File.saveString('test test', 'test.txt')
content = File.openAsString('test.txt')
self.assertEquals(content, 'test test\n')
def testSeparator(self):
sep = File.separator
self.assertEquals(sep=="/" or sep=='\\', True)
class FillTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All");
imp = newImage("test", "8-bit black", 256, 256, 1);
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All");
def testFill(self):
IJ.setForegroundColor(255, 255, 255)
imp = fill()
mean = IJ.getValue(imp, 'Mean')
self.assertEquals(mean, 255)
run("Close All");
newImage("test", "8-bit black", 256, 256, 1);
IJ.makeRectangle(64, 64, 128, 128)
imp = fill()
IJ.run("Select None")
mean = IJ.getValue(imp, 'Mean')
self.assertEquals(mean, 63.75)
def testFillOval(self):
IJ.setForegroundColor(255, 255, 255)
fillOval(128, 128, 50, 50);
roi = doWand(150, 150)
self.assertEquals(len(roi.getContainedPoints()), 1976)
def testFillRect(self):
IJ.setForegroundColor(255, 255, 255)
fillRect(128, 128, 50, 50);
roi = doWand(150, 150)
self.assertEquals(len(roi.getContainedPoints()), 2500)
class FitTest(unittest.TestCase):
def testDoFit(self):
x = [0, 1, 2, 3, 4, 5]
y = [0, 0.9, 4.5, 8, 18, 24]
Fit.doFit("Straight Line", x, y)
a = round(Fit.p(0), 4)
b = round(Fit.p(1), 4)
self.assertEquals(a, -3.2524)
self.assertEquals(b, 4.9943)
x = [0, 1, 2, 3]
y = [0, 1, 0, -1]
equation = "y = a * sin(b*x+c)"
Fit.doFit(equation, x, y)
a = round(Fit.p(0), 4)
b = round(Fit.p(1), 4)
c = round(Fit.p(2), 4)
self.assertEquals(a, 1.0000)
self.assertEquals(b, 1.5708)
self.assertEquals(c, 0.0000)
x = [0, 1, 2, 3]
y = [0, 1, 0, -1]
equation = "y = a * sin(b*x+c)"
Fit.doFit(equation, x, y, [1, 1.2, 0])
a = round(Fit.p(0), 4)
b = round(Fit.p(1), 4)
c = round(Fit.p(2), 4)
self.assertEquals(a, 1.0000)
self.assertEquals(b, 1.5708)
self.assertEquals(c, 0.0000)
def testRSquared(self):
x = [0, 1, 2, 3, 4, 5]
y = [0, 0.9, 4.5, 8, 18, 24]
Fit.doFit("Straight Line", x, y)
rSq = round(Fit.rSquared, 4)
self.assertEquals(rSq, 0.9218)
def testP(self):
x = [0, 1]
y = [-1, 0]
Fit.doFit("Straight Line", x, y) # y = a + b*x
a = Fit.p(0)
b = Fit.p(1)
self.assertEquals(a, -1)
self.assertEquals(b, 1)
def testNParams(self):
x = [0, 1, 2, 3]
y = [0, 1, 0, -1]
equation = "y = a * sin(b*x+c)"
Fit.doFit(equation, x, y, [1, 1.2, 0])
self.assertEquals(Fit.nParams, 3)
def testF(self):
x = [0, 1]
y = [-1, 0]
Fit.doFit("Straight Line", x, y) # y = a + b*x
f2 = Fit.f(2)
f3 = Fit.f(3)
self.assertEquals(f2, 1)
self.assertEquals(f3, 2)
def testNEquations(self):
self.assertEquals(Fit.nEquations>=25, True)
def testGetEquation(self):
name, formula = Fit.getEquation(0)
self.assertEquals(name, 'Straight Line')
self.assertEquals(formula, 'y = a+bx')
name, formula = Fit.getEquation(4)
self.assertEquals(name, 'Exponential')
self.assertEquals(formula, 'y = a*exp(bx)')
def testPlot(self):
x = [0, 1, 2, 3]
y = [0, 1, 0, -1]
equation = "y = a * sin(b*x+c)"
Fit.doFit(equation, x, y)
Fit.plot
title = IJ.getImage().getTitle()
self.assertEquals(title, equation)
close()
def testLogResults(self):
print('\\Clear')
Fit.logResults
x = [0, 1, 2, 3]
y = [0, 1, 0, -1]
equation = "y = a * sin(b*x+c)"
Fit.doFit(equation, x, y)
content = IJ.getLog()
lines = content.split("\n")
self.assertEquals(lines[1], 'Formula: ' + equation)
print('\\Clear')
class FloodFillTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
run("Close All")
def tearDown(self):
unittest.TestCase.tearDown(self)
run("Close All")
IJ.setForegroundColor(255, 255, 255);
def testFloodFill4(self):
imp = newImage("test", "RGB black", 256, 256, 1);
IJ.makeRectangle(10, 10, 100, 100)
IJ.setForegroundColor(255, 255, 255);
run("Fill", "slice");
run("Select None");