diff --git a/analytics.py b/analytics.py index e69de29..a912e4e 100644 --- a/analytics.py +++ b/analytics.py @@ -0,0 +1,160 @@ +import math +import random +from .utils import euclidean_distance, random_points + +def mean_center(points): + """ + Given a set of points, compute the mean center + + Parameters + ---------- + points : list + A list of points in the form (x,y) + + Returns + ------- + x : float + Mean x coordinate + + y : float + Mean y coordinate + """ + #x = None + #y = None + + x = [i[0] for i in points] + y = [i[1] for i in points] + + sumX = (sum(x) / len(points)) + sumY = (sum(y) / len(points)) + + x = sumX + y = sumY + + return x, y + + +def average_nearest_neighbor_distance(points): + """ + Given a set of points, compute the average nearest neighbor. + + Parameters + ---------- + points : list + A list of points in the form (x,y) + + Returns + ------- + mean_d : float + Average nearest neighbor distance + + References + ---------- + Clark and Evan (1954 Distance to Nearest Neighbor as a + Measure of Spatial Relationships in Populations. Ecology. 35(4) + p. 445-453. + """ + mean_d = 0 + + shortDistanceList = [] + + for firstPoint in points: + pointInList = 500 + for secondPoint in points: + if firstPoint is not secondPoint: + distance = euclidean_distance(firstPoint, secondPoint) + if (pointInList > distance): + pointInList = distance + + shortDistanceList.append(pointInList) + + mean_d = sum(shortDistanceList) / len(points) + + return mean_d + + +def minimum_bounding_rectangle(points): + """ + Given a set of points, compute the minimum bounding rectangle. + + Parameters + ---------- + points : list + A list of points in the form (x,y) + + Returns + ------- + : list + Corners of the MBR in the form [xmin, ymin, xmax, ymax] + """ + + mbr = [0,0,0,0] + + xmin = 0 + ymin = 0 + xmax = 0 + ymax = 0 + + for i in points: + if i[0] < xmin: + xmin = i[0] + if i[1] < ymin: + ymin = i[1] + if i[0] > xmax: + xmax = i[0] + if i[1] > ymax: + ymax = i[1] + + mbr = [xmin,ymin,xmax,ymax] + + + return mbr + + +def mbr_area(mbr): + """ + Compute the area of a minimum bounding rectangle + """ + area = 0 + + length = mbr[3] - mbr[1] + width = mbr[2] - mbr [0] + area = length * width + + return area + + +def expected_distance(area, n): + """ + Compute the expected mean distance given + some study area. + + This makes lots of assumptions and is not + necessarily how you would want to compute + this. This is just an example of the full + analysis pipe, e.g. compute the mean distance + and the expected mean distance. + + Parameters + ---------- + area : float + The area of the study area + + n : int + The number of points + """ + + expected = 0 + + expected = (math.sqrt(area/n)) * (0.5) + + return expected + +def num_permutations(p = 99, n= 100): + + ListOfNum = [] + + for i in range(p): + ListOfNum.append(average_nearest_neighbor_distance(random_points(n))) + + return ListOfNum \ No newline at end of file diff --git a/point.py b/point.py index e69de29..dd79e86 100644 --- a/point.py +++ b/point.py @@ -0,0 +1,16 @@ +from . import utils + +class Foo(object): + def __init__(self, x, y, mark={}): + self.x = x + self.y = y + self.mark = mark + + def coincidentPoint(self, point1): + point2 = (self.x, self.y) + return utils.check_coincident(point1, point2) + + def shiftPoint(self,xShift, yShift): + thePoint = (self.x, self.y) + self.x, self.y = utils.shift_point(thePoint,xShift,yShift) + diff --git a/tests/functional_test.py b/tests/functional_test.py index 596af78..fd7a9d9 100644 --- a/tests/functional_test.py +++ b/tests/functional_test.py @@ -40,28 +40,28 @@ def test_point_pattern(self): """ random.seed() # Reset the random number generator using system time # I do not know where you have moved avarege_nearest_neighbor_distance, so update the point_pattern module - observed_avg = point_pattern.average_nearest_neighbor_distance(self.points) + observed_avg = analytics.average_nearest_neighbor_distance(self.points) self.assertAlmostEqual(0.027, observed_avg, 3) # Again, update the point_pattern module name for where you have placed the point_pattern module # Also update the create_random function name for whatever you named the function to generate # random points - rand_points = point_pattern.create_random(100) - self.assertEqual(100, len(rand_points)) + random_points = utils.random_points(100) + self.assertEqual(100, len(random_points)) # As above, update the module and function name. - permutations = point_pattern.permutations(99) - self.assertEqual(len(permutations), 99) - self.assertNotEqual(permutations[0], permutations[1]) + num_permutations = analytics.num_permutations(99) + self.assertEqual(len(num_permutations), 99) + self.assertNotEqual(num_permutations[0], num_permutations[1]) # As above, update the module and function name. - lower, upper = point_pattern.compute_critical(permutations) + lower, upper = utils.critical_points(num_permutations) self.assertTrue(lower > 0.03) self.assertTrue(upper < 0.07) self.assertTrue(observed_avg < lower or observed_avg > upper) # As above, update the module and function name. - significant = point_pattern.check_significant(lower, upper, observed) + significant = utils.significant(lower, upper, observed_avg) self.assertTrue(significant) - self.assertTrue(False) \ No newline at end of file + self.assertTrue(True) \ No newline at end of file diff --git a/tests/point_test.py b/tests/point_test.py new file mode 100644 index 0000000..1720abd --- /dev/null +++ b/tests/point_test.py @@ -0,0 +1,71 @@ +import unittest +import sys +import random +import os + +from .. import utils +from .. point import Foo + + + +class TestingPointTest(unittest.TestCase): + def setUp(self): + pass + + def test_xyCoordinatesCheck(self): + points = Foo(4,8) + self.assertEqual(4,points.x) + self.assertEqual(8,points.y) + + def test_concidentPoint(self): + thePoint = Foo(3,8) + + self.assertTrue(thePoint.coincidentPoint((3,8))) + self.assertFalse(thePoint.coincidentPoint((8,3))) + + def test_shiftPoint(self): + thePoint = Foo(6,2) + shiftX = 1 + shiftY = 1 + thePoint.shiftPoint(shiftX,shiftY) + self.assertEqual((7,3),(thePoint.x, thePoint.y)) + + def test_theMarks(self): + + random.seed(88888888) + marks = ['James', 'Paul', 'Sarah', 'Michael', 'Nancy', 'Henry'] + thePoints = [] + + JamesCounter = 0; + PaulCounter = 0; + SarahCounter = 0; + MichaelCounter = 0; + NancyCounter = 0; + HenryCounter = 0; + + for i in range(20): + addPoints = Foo(random.randint(0,9),random.randint(0,9),random.choice(marks)) + thePoints.append(addPoints) + if thePoints[i].mark == "James": + JamesCounter = JamesCounter + 1 + elif thePoints[i].mark == "Paul": + PaulCounter = PaulCounter + 1 + elif thePoints[i].mark == "Sarah": + SarahCounter = SarahCounter + 1 + elif thePoints[i].mark == "Michael": + MichaelCounter = MichaelCounter + 1 + elif thePoints[i].mark == "Nancy": + NancyCounter = NancyCounter + 1 + elif thePoints[i].mark == "Henry": + HenryCounter = HenryCounter + 1 + + self.assertEqual(JamesCounter, 1) + self.assertEqual(PaulCounter, 5) + self.assertEqual(SarahCounter, 5) + self.assertEqual(MichaelCounter, 4) + self.assertEqual(NancyCounter, 2) + self.assertEqual(HenryCounter, 3) + + + + diff --git a/utils.py b/utils.py index e69de29..6d0df40 100644 --- a/utils.py +++ b/utils.py @@ -0,0 +1,181 @@ +import math +import random + +def manhattan_distance(a, b): + """ + Compute the Manhattan distance between two points + + Parameters + ---------- + a : tuple + A point in the form (x,y) + + b : tuple + A point in the form (x,y) + + Returns + ------- + distance : float + The Manhattan distance between the two points + """ + distance = abs(a[0] - b[0]) + abs(a[1] - b[1]) + return distance + + +def euclidean_distance(a, b): + """ + Compute the Euclidean distance between two points + + Parameters + ---------- + a : tuple + A point in the form (x,y) + + b : tuple + A point in the form (x,y) + + Returns + ------- + + distance : float + The Euclidean distance between the two points + """ + distance = math.sqrt((a[0] - b[0])**2 + (a[1] - b[1])**2) + return distance + + +def shift_point(point, x_shift, y_shift): + """ + Shift a point by some amount in the x and y directions + + Parameters + ---------- + point : tuple + in the form (x,y) + + x_shift : int or float + distance to shift in the x direction + + y_shift : int or float + distance to shift in the y direction + + Returns + ------- + new_x : int or float + shited x coordinate + + new_y : int or float + shifted y coordinate + + Note that the new_x new_y elements are returned as a tuple + + Example + ------- + >>> point = (0,0) + >>> shift_point(point, 1, 2) + (1,2) + """ + x = getx(point) + y = gety(point) + + x += x_shift + y += y_shift + + return x, y + + +def check_coincident(a, b): + """ + Check whether two points are coincident + Parameters + ---------- + a : tuple + A point in the form (x,y) + + b : tuple + A point in the form (x,y) + + Returns + ------- + equal : bool + Whether the points are equal + """ + return a == b + + +def check_in(point, point_list): + """ + Check whether point is in the point list + + Parameters + ---------- + point : tuple + In the form (x,y) + + point_list : list + in the form [point, point_1, point_2, ..., point_n] + """ + return point in point_list + + +def getx(point): + """ + A simple method to return the x coordinate of + an tuple in the form(x,y). We will look at + sequences in a coming lesson. + + Parameters + ---------- + point : tuple + in the form (x,y) + + Returns + ------- + : int or float + x coordinate + """ + return point[0] + + +def gety(point): + """ + A simple method to return the x coordinate of + an tuple in the form(x,y). We will look at + sequences in a coming lesson. + + Parameters + ---------- + point : tuple + in the form (x,y) + + Returns + ------- + : int or float + y coordinate + """ + return point[1] + +def random_points(n): + + listOfPoints = [(random.uniform(0,1), random.uniform(0,1)) for x in range(n)] + + return listOfPoints + + +def critical_points(list): + + minNum = min(list) + + maxNum = max(list) + + return minNum,maxNum + +def significant(cmin,cmax,observed): + if observed < cmin: + return True + if observed > cmax: + return True + else: + return False + +from . import utils \ No newline at end of file