# Simpson College MATH 290 Spring 2021 - PowerPollen Research
# Authors: Georgia Porter, Eli Marriott, Alyssa Whitham, Ethan Humble
# PowerPollen Mentor Contacts: Cheng Pan, Alex Austin
# Advisor: Ross Sweet
# Deepnote setup
!apt update
!apt install ffmpeg libsm6 libxext6 -y
!pip install xlrd
!pip install openpyxl
# Imports
import math
import os
import re
import time
import scipy.stats
import cv2
import imutils
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
# Function to compute the number of grains in an image. Input file name and directory.
# Output is an integer count.
def grain_counter(fname, direc):
f = os.path.join(direc, fname)
resizeHeight = 1000
im = cv2.imread(f)
im = imutils.resize(im, height=resizeHeight)
im = cv2.cvtColor(im, cv2.COLOR_BGR2GRAY)
im = cv2.blur(im, (9, 9))
ret, binary1 = cv2.threshold(im, 80, 255, cv2.THRESH_BINARY_INV)
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (5, 1))
closed = cv2.morphologyEx(binary1, cv2.MORPH_CLOSE, kernel)
contours1, _ = cv2.findContours(closed, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
grains = 0
minimum_area = 900
connected_grain_area = 2800
temp = 0
for i in contours1:
area = cv2.contourArea(i)
if area > minimum_area:
if area > connected_grain_area:
temp = area/connected_grain_area
temp = math.ceil(temp)
# Assumption of rounding up
grains += temp
else:
grains += 1
return(grains)
# Vectorize the grain_counter function.
vgrain_counter = np.vectorize(grain_counter)
# Function to plot the original image and the image with contours of grains added.
# Input is a file name and directory, output is a pair of captioned images.
def grain_imager(fname, direc):
f = os.path.join(direc, fname)
resizeHeight = 1000
im = cv2.imread(f)
im = imutils.resize(im, height=resizeHeight)
im2 = im.copy()
gray1 = cv2.cvtColor(im, cv2.COLOR_BGR2GRAY)
blurred1 = cv2.blur(gray1, (9, 9))
ret, binary1 = cv2.threshold(blurred1, 80, 255, cv2.THRESH_BINARY_INV)
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (5, 1))
closed = cv2.morphologyEx(binary1, cv2.MORPH_CLOSE, kernel)
contours1, _ = cv2.findContours(closed, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
minimum_area = 900
connected_grain_area = 2800
temp = 0
grains = 0
for i in contours1:
area = cv2.contourArea(i)
if area > minimum_area:
cv2.drawContours(im, [i], -1, (0, 255, 0), 5)
if area > connected_grain_area:
temp = area/connected_grain_area
temp = math.ceil(temp)
# Assumption of rounding up
grains += temp
else:
grains += 1
text = "Pollen Grains:{grains}.".format(grains=grains)
dy = 30
y0 = resizeHeight - dy
for i, line in enumerate(text.split('\n')):
y = y0 + i*dy
counted = cv2.putText(im, line, (10, y),
cv2.FONT_HERSHEY_DUPLEX, 1, (255, 0, 0), 3)
titles = ["Original Image", "Counted"]
images = [im2, counted]
plt.figure(figsize=(20,12))
for i in range(2):
plt.subplot(2,3,i+1),plt.imshow(images[i])
plt.title(titles[i])
plt.xticks([]),plt.yticks([])
return(plt.draw())
def tube_counter(fname, direc, match_im):
resizeHeight = 1000
tubecount = 0
min_max_list = list()
# Read comparison image and test image
f = os.path.join(direc, fname)
img1 = cv2.imread(match_im)
img1 = imutils.resize(img1, height=resizeHeight)
img2 = cv2.imread(f)
img2 = imutils.resize(img2, height=resizeHeight)
# Convert to grayscale
gray1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY)
gray2 = cv2.cvtColor(img2, cv2.COLOR_BGR2GRAY)
# Sharpen Image
gaussian_3 = cv2.GaussianBlur(gray2, (0,0), 2.0)
gray2 = cv2.addWeighted(gray2, 1.5, gaussian_3, -0.25, -30)
points = sns.kdeplot(gray2.ravel(), cut = 0).get_lines()[0].get_data() # pull point data from density plot
combined = pd.DataFrame(np.column_stack(points),columns=['x','y']) # format point data as data frame
resizeWidth = img2.shape[1]
numPixels = resizeHeight * resizeWidth
combined['freq'] = combined['y'] * numPixels
freqCutoff = 950 # Set the cutoff value for pixel value frequency
lower = (combined['freq'] < freqCutoff) & (combined.shift()['freq'] > freqCutoff)
upper = (combined['freq'] < freqCutoff) & (combined.shift(-1)['freq'] > freqCutoff)
min_max = combined[lower | upper] # Filter for index differences larger than one
if min_max.shape[0] == 3:
minPixel = min_max.iloc[0]['x']
maxPixel = min_max.iloc[1]['x']
elif min_max.shape[0] == 4:
minPixel = min_max.iloc[1]['x']
maxPixel = min_max.iloc[2]['x']
else:
minPixel = 50
maxPixel = 150
# Threshold Images using MIN & MAX
blurred1 = cv2.blur(gray1, (9, 9))
ret, binary1 = cv2.threshold(blurred1, 80, 255, cv2.THRESH_BINARY_INV)
binary2 = cv2.inRange(gray2, minPixel, maxPixel)
# Find contours
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (5, 1))
closed1 = cv2.morphologyEx(binary1, cv2.MORPH_CLOSE, kernel)
closed2 = cv2.morphologyEx(binary2, cv2.MORPH_CLOSE, kernel)
contours1, _ = cv2.findContours(closed1,cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
cnt1 = contours1[0]
contours2, _ = cv2.findContours(closed2,cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
# Run MatchShape function
for i in contours2:
perimeter = cv2.arcLength(i, True)
area = cv2.contourArea(i)
testreturn = cv2.matchShapes(cnt1, i, 1, 0.0)
if testreturn > 1 and testreturn < 1000 and area > 400:
cv2.drawContours(img2, [i], -1, (0, 255, 0), 5)
tubecount += 1
return(tubecount)
# Vectorize the tube_counter function.
vtube_counter = np.vectorize(tube_counter)
# Tube count visualization
def tube_imager(fname, direc, match_im):
# Variables
resizeHeight = 1000
tubecount = 0
min_max_list = list()
# Read comparison image and test image
f = os.path.join(direc, fname)
img1 = cv2.imread(match_im)
img1 = imutils.resize(img1, height=resizeHeight)
img2 = cv2.imread(f)
img2 = imutils.resize(img2, height=resizeHeight)
img2_orig = img2.copy()
# Convert to grayscale
gray1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY)
gray2 = cv2.cvtColor(img2, cv2.COLOR_BGR2GRAY)
# Sharpen Image
gaussian_3 = cv2.GaussianBlur(gray2, (0,0), 2.0)
gray2 = cv2.addWeighted(gray2, 1.5, gaussian_3, -0.25, -30)
points = sns.kdeplot(gray2.ravel(), cut = 0).get_lines()[0].get_data() # pull point data from density plot
combined = pd.DataFrame(np.column_stack(points),columns=['x','y']) # format point data as data frame
resizeWidth = img2.shape[1]
numPixels = resizeHeight * resizeWidth
combined['freq'] = combined['y'] * numPixels
freqCutoff = 950 # Set the cutoff value for pixel value frequency
lower = (combined['freq'] < freqCutoff) & (combined.shift()['freq'] > freqCutoff)
upper = (combined['freq'] < freqCutoff) & (combined.shift(-1)['freq'] > freqCutoff)
min_max = combined[lower | upper] # Filter for index differences larger than one
if min_max.shape[0] == 3:
minPixel = min_max.iloc[0]['x']
maxPixel = min_max.iloc[1]['x']
elif min_max.shape[0] == 4:
minPixel = min_max.iloc[1]['x']
maxPixel = min_max.iloc[2]['x']
else:
minPixel = 50
maxPixel = 150
# Threshold Images using MIN & MAX
blurred1 = cv2.blur(gray1, (9, 9))
ret, binary1 = cv2.threshold(blurred1, 80, 255, cv2.THRESH_BINARY_INV)
binary2 = cv2.inRange(gray2, minPixel, maxPixel)
# Find contours
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (5, 1))
closed1 = cv2.morphologyEx(binary1, cv2.MORPH_CLOSE, kernel)
closed2 = cv2.morphologyEx(binary2, cv2.MORPH_CLOSE, kernel)
contours1, _ = cv2.findContours(closed1,cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
cnt1 = contours1[0]
contours2, _ = cv2.findContours(closed2,cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
# Run MatchShape function
for i in contours2:
perimeter = cv2.arcLength(i, True)
area = cv2.contourArea(i)
testreturn = cv2.matchShapes(cnt1, i, 1, 0.0)
if testreturn > 1 and testreturn < 1000 and area > 400:
cv2.drawContours(img2, [i], -1, (0, 255, 0), 5)
tubecount += 1
text = "Tube count:{testreturn}.".format(testreturn=testreturn)
dy = 30
y0 = resizeHeight - dy
for i, line in enumerate(text.split('\n')):
y = y0 + i*dy
counted = cv2.putText(img2, line, (10, y),cv2.FONT_HERSHEY_DUPLEX, 1, (0, 0, 25), 3)
# Plot step by step images in a grid
titles = ["Original Image", "Counted"]
images = [img2_orig, counted]
plt.figure(figsize=(20,12))
for i in range(2):
plt.subplot(2,3,i+1),plt.imshow(images[i])
plt.title(titles[i])
plt.xticks([]),plt.yticks([])
return(plt.draw())
#Run Grain Counter
directory = '/work/Math290Spring2021/Pure'
pure_data = pd.read_excel('/work/Math290Spring2021/Image_count_result.xlsx',
sheet_name='Pure',
engine = 'openpyxl')
match = '/work/Pure (1)-Cropped.tif'
df = pd.DataFrame(os.listdir(directory), columns = ['FileName']) # Create data frame of file names.
df['Sample'] = df['FileName'].str.extract('\(([^)]+)') # Make column with just sample number.
df = df.dropna() # Drop missing values corresponding to non-sample files, e.g., Readme
df['Sample'] = df['Sample'].astype(str).astype(int) # Convert sample column to integer.
df['est_grain'] = vgrain_counter(df['FileName'], directory) # Compute estimated number of grains for each sample.
df = pd.merge(df, pure_data[['Sample', 'Total Pollen', 'with Tube']], on = 'Sample', how = 'left') # Merge with actual counts from Excel file.
df['fracdiff_grain'] = (df['est_grain'] - df['Total Pollen']) / df['Total Pollen'] # Compute the fractional difference in estimated and true counts.
df['absfracdiff_grain'] = df['fracdiff_grain'].abs()
print(df['absfracdiff_grain'].describe()) # Summary statistics of the fractional differences.
plt.figure()
df['absfracdiff_grain'].hist(bins = 20) # Plot histogram of fractional differences.
plt.figure()
df.boxplot(column='absfracdiff_grain') # Print boxplot of fractional differences.
grain_imager("Pure (23).tif", directory) # View sample image and counted grains.
#Run Tube Counter
df['est_tube'] = vtube_counter(df['FileName'], directory, match)
df['fracdiff_tube'] = (df['est_tube'] - df['with Tube']) / df['with Tube']
df_wtubes = df
df['absfdiff_tube'] = df['fracdiff_tube'].abs()
print(df['absfdiff_tube'].describe()) # Summary statistics of the fractional differences.
plt.figure()
df['absfdiff_tube'].hist(bins = 20) # Plot histogram of fractional differences.
plt.figure()
df.boxplot(column='absfdiff_tube') # Print boxplot of fractional differences.
print(df.to_string())
tube_imager('Pure (72).tif', directory, match)
print(df_wtubes['fracdiff_tube'].abs().median())
print(df_wtubes['fracdiff_grain'].abs().median())
Get:1 http://security.debian.org/debian-security buster/updates InRelease [65.4 kB]
Get:2 http://deb.debian.org/debian buster InRelease [121 kB]
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Get:4 http://security.debian.org/debian-security buster/updates/main amd64 Packages [272 kB]
Get:5 http://deb.debian.org/debian buster/main amd64 Packages [7,907 kB]
Get:6 http://deb.debian.org/debian buster-updates/main amd64 Packages [10.9 kB]
Fetched 8,428 kB in 3s (3,273 kB/s)
21 packages can be upgraded. Run 'apt list --upgradable' to see them.
libsm6 is already the newest version (2:1.2.3-1).
libsm6 set to manually installed.
libxext6 is already the newest version (2:1.3.3-1+b2).
libxext6 set to manually installed.
The following additional packages will be installed:
i965-va-driver intel-media-va-driver libaacs0 libaom0 libasound2
libasound2-data libass9 libasyncns0 libavc1394-0 libavcodec58 libavdevice58
libavfilter7 libavformat58 libavresample4 libavutil56 libbdplus0 libbluray2
libbs2b0 libcaca0 libcap2 libcdio-cdda2 libcdio-paranoia2 libcdio18
libchromaprint1 libcodec2-0.8.1 libcrystalhd3 libdc1394-22 libdrm-amdgpu1
libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2
libfftw3-double3 libflac8 libflite1 libgl1 libgl1-mesa-dri libglapi-mesa
libglvnd0 libglx-mesa0 libglx0 libgme0 libgsm1 libiec61883-0 libigdgmm5
libjack-jackd2-0 liblilv-0-0 libllvm7 libmp3lame0 libmpg123-0 libmysofa0
libnorm1 libnuma1 libogg0 libopenal-data libopenal1 libopenjp2-7 libopenmpt0
libopus0 libpciaccess0 libpgm-5.2-0 libpostproc55 libpulse0 libraw1394-11
librubberband2 libsamplerate0 libsdl2-2.0-0 libsensors-config libsensors5
libserd-0-0 libshine3 libslang2 libsnappy1v5 libsndfile1 libsndio7.0
libsodium23 libsord-0-0 libsoxr0 libspeex1 libsratom-0-0 libssh-gcrypt-4
libswresample3 libswscale5 libtheora0 libtwolame0 libusb-1.0-0 libva-drm2
libva-x11-2 libva2 libvdpau-va-gl1 libvdpau1 libvidstab1.1 libvorbis0a
libvorbisenc2 libvorbisfile3 libvpx5 libwavpack1 libwayland-client0
libwayland-cursor0 libwayland-egl1 libwebpmux3 libx11-xcb1 libx264-155
libx265-165 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-shape0 libxcb-sync1 libxcb-xfixes0 libxkbcommon0 libxshmfence1
libxss1 libxtst6 libxv1 libxvidcore4 libxxf86vm1 libzmq5 libzvbi-common
libzvbi0 mesa-va-drivers mesa-vdpau-drivers va-driver-all vdpau-driver-all
xkb-data
Suggested packages:
ffmpeg-doc i965-va-driver-shaders libasound2-plugins alsa-utils
libbluray-bdj firmware-crystalhd libfftw3-bin libfftw3-dev jackd2
libportaudio2 opus-tools pciutils pulseaudio libraw1394-doc lm-sensors serdi
sndiod sordi speex nvidia-vdpau-driver nvidia-legacy-340xx-vdpau-driver
nvidia-legacy-304xx-vdpau-driver
The following NEW packages will be installed:
ffmpeg i965-va-driver intel-media-va-driver libaacs0 libaom0 libasound2
libasound2-data libass9 libasyncns0 libavc1394-0 libavcodec58 libavdevice58
libavfilter7 libavformat58 libavresample4 libavutil56 libbdplus0 libbluray2
libbs2b0 libcaca0 libcap2 libcdio-cdda2 libcdio-paranoia2 libcdio18
libchromaprint1 libcodec2-0.8.1 libcrystalhd3 libdc1394-22 libdrm-amdgpu1
libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2
libfftw3-double3 libflac8 libflite1 libgl1 libgl1-mesa-dri libglapi-mesa
libglvnd0 libglx-mesa0 libglx0 libgme0 libgsm1 libiec61883-0 libigdgmm5
libjack-jackd2-0 liblilv-0-0 libllvm7 libmp3lame0 libmpg123-0 libmysofa0
libnorm1 libnuma1 libogg0 libopenal-data libopenal1 libopenjp2-7 libopenmpt0
libopus0 libpciaccess0 libpgm-5.2-0 libpostproc55 libpulse0 libraw1394-11
librubberband2 libsamplerate0 libsdl2-2.0-0 libsensors-config libsensors5
libserd-0-0 libshine3 libslang2 libsnappy1v5 libsndfile1 libsndio7.0
libsodium23 libsord-0-0 libsoxr0 libspeex1 libsratom-0-0 libssh-gcrypt-4
libswresample3 libswscale5 libtheora0 libtwolame0 libusb-1.0-0 libva-drm2
libva-x11-2 libva2 libvdpau-va-gl1 libvdpau1 libvidstab1.1 libvorbis0a
libvorbisenc2 libvorbisfile3 libvpx5 libwavpack1 libwayland-client0
libwayland-cursor0 libwayland-egl1 libwebpmux3 libx11-xcb1 libx264-155
libx265-165 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-shape0 libxcb-sync1 libxcb-xfixes0 libxkbcommon0 libxshmfence1
libxss1 libxtst6 libxv1 libxvidcore4 libxxf86vm1 libzmq5 libzvbi-common
libzvbi0 mesa-va-drivers mesa-vdpau-drivers va-driver-all vdpau-driver-all
xkb-data
0 upgraded, 128 newly installed, 0 to remove and 21 not upgraded.
Need to get 64.2 MB of archives.
After this operation, 379 MB of additional disk space will be used.
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Get:29 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB]
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Get:45 http://deb.debian.org/debian buster/main amd64 libopenmpt0 amd64 0.4.3-1+deb10u1 [627 kB]
Get:46 http://deb.debian.org/debian buster/main amd64 libssh-gcrypt-4 amd64 0.8.7-1+deb10u1 [200 kB]
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Get:48 http://deb.debian.org/debian buster/main amd64 libbs2b0 amd64 3.1.0+dfsg-2.2 [12.2 kB]
Get:49 http://deb.debian.org/debian buster/main amd64 libflite1 amd64 2.1-release-3 [12.8 MB]
Get:50 http://deb.debian.org/debian buster/main amd64 libserd-0-0 amd64 0.28.0~dfsg0-1 [40.8 kB]
Get:51 http://deb.debian.org/debian buster/main amd64 libsord-0-0 amd64 0.16.0~dfsg0-1+b1 [23.0 kB]
Get:52 http://deb.debian.org/debian buster/main amd64 libsratom-0-0 amd64 0.6.0~dfsg0-1 [16.6 kB]
Get:53 http://deb.debian.org/debian buster/main amd64 liblilv-0-0 amd64 0.24.2~dfsg0-2 [44.2 kB]
Get:54 http://deb.debian.org/debian buster/main amd64 libmysofa0 amd64 0.6~dfsg0-3+deb10u1 [38.2 kB]
Get:55 http://deb.debian.org/debian buster/main amd64 libpostproc55 amd64 7:4.1.6-1~deb10u1 [101 kB]
Get:56 http://deb.debian.org/debian buster/main amd64 libfftw3-double3 amd64 3.3.8-2 [733 kB]
Get:57 http://deb.debian.org/debian buster/main amd64 libsamplerate0 amd64 0.1.9-2 [949 kB]
Get:58 http://deb.debian.org/debian buster/main amd64 librubberband2 amd64 1.8.1-7 [86.0 kB]
Get:59 http://deb.debian.org/debian buster/main amd64 libswscale5 amd64 7:4.1.6-1~deb10u1 [202 kB]
Get:60 http://deb.debian.org/debian buster/main amd64 libvidstab1.1 amd64 1.1.0-2 [37.6 kB]
Get:61 http://deb.debian.org/debian buster/main amd64 libnorm1 amd64 1.5.8+dfsg2-1 [287 kB]
Get:62 http://deb.debian.org/debian buster/main amd64 libpgm-5.2-0 amd64 5.2.122~dfsg-3 [158 kB]
Get:63 http://deb.debian.org/debian buster/main amd64 libsodium23 amd64 1.0.17-1 [158 kB]
Get:64 http://deb.debian.org/debian buster/main amd64 libzmq5 amd64 4.3.1-4+deb10u2 [246 kB]
Get:65 http://deb.debian.org/debian buster/main amd64 libavfilter7 amd64 7:4.1.6-1~deb10u1 [1,046 kB]
Get:66 http://deb.debian.org/debian buster/main amd64 libslang2 amd64 2.3.2-2 [507 kB]
Get:67 http://deb.debian.org/debian buster/main amd64 libcaca0 amd64 0.99.beta19-2.1 [346 kB]
Get:68 http://deb.debian.org/debian buster/main amd64 libcdio18 amd64 2.0.0-2 [199 kB]
Get:69 http://deb.debian.org/debian buster/main amd64 libcdio-cdda2 amd64 10.2+0.94+2-4 [26.4 kB]
Get:70 http://deb.debian.org/debian buster/main amd64 libcdio-paranoia2 amd64 10.2+0.94+2-4 [27.8 kB]
Get:71 http://deb.debian.org/debian buster/main amd64 libusb-1.0-0 amd64 2:1.0.22-2 [55.3 kB]
Get:72 http://deb.debian.org/debian buster/main amd64 libdc1394-22 amd64 2.2.5-1 [106 kB]
Get:73 http://deb.debian.org/debian buster/main amd64 libglvnd0 amd64 1.1.0-1 [48.6 kB]
Get:74 http://deb.debian.org/debian buster/main amd64 libglapi-mesa amd64 18.3.6-2+deb10u1 [66.3 kB]
Get:75 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1+deb10u1 [190 kB]
Get:76 http://deb.debian.org/debian buster/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB]
Get:77 http://deb.debian.org/debian buster/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB]
Get:78 http://deb.debian.org/debian buster/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB]
Get:79 http://deb.debian.org/debian buster/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB]
Get:80 http://deb.debian.org/debian buster/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB]
Get:81 http://deb.debian.org/debian buster/main amd64 libxshmfence1 amd64 1.3-1 [8,820 B]
Get:82 http://deb.debian.org/debian buster/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get:83 http://deb.debian.org/debian buster/main amd64 libdrm-amdgpu1 amd64 2.4.97-1 [27.3 kB]
Get:84 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB]
Get:85 http://deb.debian.org/debian buster/main amd64 libdrm-intel1 amd64 2.4.97-1 [69.8 kB]
Get:86 http://deb.debian.org/debian buster/main amd64 libdrm-nouveau2 amd64 2.4.97-1 [26.3 kB]
Get:87 http://deb.debian.org/debian buster/main amd64 libdrm-radeon1 amd64 2.4.97-1 [31.1 kB]
Get:88 http://deb.debian.org/debian buster/main amd64 libllvm7 amd64 1:7.0.1-8+deb10u2 [13.1 MB]
Get:89 http://deb.debian.org/debian buster/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB]
Get:90 http://deb.debian.org/debian buster/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB]
Get:91 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-dri amd64 18.3.6-2+deb10u1 [6,685 kB]
Get:92 http://deb.debian.org/debian buster/main amd64 libglx-mesa0 amd64 18.3.6-2+deb10u1 [180 kB]
Get:93 http://deb.debian.org/debian buster/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB]
Get:94 http://deb.debian.org/debian buster/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB]
Get:95 http://deb.debian.org/debian buster/main amd64 libiec61883-0 amd64 1.2.0-3 [31.2 kB]
Get:96 http://deb.debian.org/debian buster/main amd64 libjack-jackd2-0 amd64 1.9.12~dfsg-2 [299 kB]
Get:97 http://deb.debian.org/debian buster/main amd64 libopenal-data all 1:1.19.1-1 [170 kB]
Get:98 http://deb.debian.org/debian buster/main amd64 libsndio7.0 amd64 1.5.0-3 [24.7 kB]
Get:99 http://deb.debian.org/debian buster/main amd64 libopenal1 amd64 1:1.19.1-1 [500 kB]
Get:100 http://deb.debian.org/debian buster/main amd64 libasyncns0 amd64 0.8-6 [12.5 kB]
Get:101 http://deb.debian.org/debian buster/main amd64 libcap2 amd64 1:2.25-2 [17.6 kB]
Get:102 http://deb.debian.org/debian buster/main amd64 libflac8 amd64 1.3.2-3 [221 kB]
Get:103 http://deb.debian.org/debian buster/main amd64 libsndfile1 amd64 1.0.28-6 [253 kB]
Get:104 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB]
Get:105 http://deb.debian.org/debian buster/main amd64 libpulse0 amd64 12.2-4+deb10u1 [281 kB]
Get:106 http://deb.debian.org/debian buster/main amd64 libwayland-client0 amd64 1.16.0-1 [26.4 kB]
Get:107 http://deb.debian.org/debian buster/main amd64 libwayland-cursor0 amd64 1.16.0-1 [14.1 kB]
Get:108 http://deb.debian.org/debian buster/main amd64 libwayland-egl1 amd64 1.16.0-1 [8,204 B]
Get:109 http://deb.debian.org/debian buster/main amd64 xkb-data all 2.26-2 [681 kB]
Get:110 http://deb.debian.org/debian buster/main amd64 libxkbcommon0 amd64 0.8.2-1 [123 kB]
Get:111 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB]
Get:112 http://deb.debian.org/debian buster/main amd64 libsdl2-2.0-0 amd64 2.0.9+dfsg1-1 [401 kB]
Get:113 http://deb.debian.org/debian buster/main amd64 libxcb-shape0 amd64 1.13.1-2 [99.5 kB]
Get:114 http://deb.debian.org/debian buster/main amd64 libxcb-xfixes0 amd64 1.13.1-2 [103 kB]
Get:115 http://deb.debian.org/debian buster/main amd64 libxv1 amd64 2:1.0.11-1 [24.6 kB]
Get:116 http://deb.debian.org/debian buster/main amd64 libavdevice58 amd64 7:4.1.6-1~deb10u1 [124 kB]
Get:117 http://deb.debian.org/debian buster/main amd64 libavresample4 amd64 7:4.1.6-1~deb10u1 [102 kB]
Get:118 http://deb.debian.org/debian buster/main amd64 ffmpeg amd64 7:4.1.6-1~deb10u1 [1,434 kB]
Get:119 http://deb.debian.org/debian buster/main amd64 i965-va-driver amd64 2.3.0+dfsg1-1 [311 kB]
Get:120 http://deb.debian.org/debian buster/main amd64 libigdgmm5 amd64 18.4.1+ds1-1 [78.7 kB]
Get:121 http://deb.debian.org/debian buster/main amd64 intel-media-va-driver amd64 18.4.1+dfsg1-1 [974 kB]
Get:122 http://deb.debian.org/debian buster/main amd64 libaacs0 amd64 0.9.0-2 [52.4 kB]
Get:123 http://deb.debian.org/debian buster/main amd64 libbdplus0 amd64 0.1.2-3 [47.5 kB]
Get:124 http://deb.debian.org/debian buster/main amd64 libvdpau-va-gl1 amd64 0.4.2-1+b1 [71.3 kB]
Get:125 http://deb.debian.org/debian buster/main amd64 mesa-va-drivers amd64 18.3.6-2+deb10u1 [1,972 kB]
Get:126 http://deb.debian.org/debian buster/main amd64 mesa-vdpau-drivers amd64 18.3.6-2+deb10u1 [2,101 kB]
Get:127 http://deb.debian.org/debian buster/main amd64 va-driver-all amd64 2.4.0-1 [13.0 kB]
Get:128 http://deb.debian.org/debian buster/main amd64 vdpau-driver-all amd64 1.1.1-10 [20.8 kB]
Fetched 64.2 MB in 1s (103 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
78Selecting previously unselected package libaom0:amd64.
(Reading database ... 31088 files and directories currently installed.)
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7Progress: [ 0%] [..........................................................] 8Unpacking libaom0:amd64 (1.0.0-3) ...
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Unpacking libdrm-common (2.4.97-1) ...
Selecting previously unselected package libdrm2:amd64.
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Unpacking libdrm2:amd64 (2.4.97-1) ...
7Progress: [ 1%] [..........................................................] 8Selecting previously unselected package libva2:amd64.
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Unpacking libva2:amd64 (2.4.0-1) ...
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Unpacking libva-drm2:amd64 (2.4.0-1) ...
Selecting previously unselected package libva-x11-2:amd64.
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7Progress: [ 2%] [#.........................................................] 8Unpacking libva-x11-2:amd64 (2.4.0-1) ...
Selecting previously unselected package libvdpau1:amd64.
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Unpacking libvdpau1:amd64 (1.1.1-10) ...
Selecting previously unselected package libavutil56:amd64.
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Unpacking libavutil56:amd64 (7:4.1.6-1~deb10u1) ...
7Progress: [ 3%] [#.........................................................] 8Selecting previously unselected package libcodec2-0.8.1:amd64.
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Unpacking libcodec2-0.8.1:amd64 (0.8.1-2) ...
Selecting previously unselected package libcrystalhd3:amd64.
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Unpacking libcrystalhd3:amd64 (1:0.0~git20110715.fdd2f19-13) ...
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7Progress: [ 4%] [##........................................................] 8Unpacking libgsm1:amd64 (1.0.18-2) ...
Selecting previously unselected package libmp3lame0:amd64.
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Unpacking libmp3lame0:amd64 (3.100-2+b1) ...
Selecting previously unselected package libopenjp2-7:amd64.
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Unpacking libopenjp2-7:amd64 (2.3.0-2+deb10u2) ...
7Progress: [ 5%] [##........................................................] 8Selecting previously unselected package libopus0:amd64.
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Unpacking libopus0:amd64 (1.3-1) ...
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Unpacking libshine3:amd64 (3.1.1-2) ...
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7Progress: [ 6%] [###.......................................................] 8Unpacking libsnappy1v5:amd64 (1.1.7-1) ...
Selecting previously unselected package libspeex1:amd64.
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Unpacking libspeex1:amd64 (1.2~rc1.2-1+b2) ...
Selecting previously unselected package libsoxr0:amd64.
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Unpacking libsoxr0:amd64 (0.1.2-3) ...
7Progress: [ 7%] [####......................................................] 8Selecting previously unselected package libswresample3:amd64.
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Unpacking libogg0:amd64 (1.3.2-1+b1) ...
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Unpacking libtheora0:amd64 (1.1.1+dfsg.1-15) ...
7Progress: [ 8%] [####......................................................] 8Selecting previously unselected package libtwolame0:amd64.
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Unpacking libtwolame0:amd64 (0.3.13-4) ...
Selecting previously unselected package libvorbis0a:amd64.
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Unpacking libvorbis0a:amd64 (1.3.6-2) ...
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7Progress: [ 9%] [#####.....................................................] 8Unpacking libvorbisenc2:amd64 (1.3.6-2) ...
Selecting previously unselected package libvpx5:amd64.
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Unpacking libvpx5:amd64 (1.7.0-3+deb10u1) ...
Selecting previously unselected package libwavpack1:amd64.
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Unpacking libwavpack1:amd64 (5.1.0-6) ...
7Progress: [ 10%] [#####.....................................................] 8Selecting previously unselected package libwebpmux3:amd64.
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Unpacking libwebpmux3:amd64 (0.6.1-2) ...
Selecting previously unselected package libx264-155:amd64.
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Unpacking libx264-155:amd64 (2:0.155.2917+git0a84d98-2) ...
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7Progress: [ 11%] [######....................................................] 8Unpacking libnuma1:amd64 (2.0.12-1) ...
Selecting previously unselected package libx265-165:amd64.
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Unpacking libx265-165:amd64 (2.9-4) ...
Selecting previously unselected package libxvidcore4:amd64.
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Unpacking libxvidcore4:amd64 (2:1.3.5-1) ...
7Progress: [ 12%] [#######...................................................] 8Selecting previously unselected package libzvbi-common.
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Unpacking libzvbi-common (0.2.35-16) ...
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Unpacking libzvbi0:amd64 (0.2.35-16) ...
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7Progress: [ 13%] [#######...................................................] 8Unpacking libavcodec58:amd64 (7:4.1.6-1~deb10u1) ...
Selecting previously unselected package libasound2-data.
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Unpacking libasound2-data (1.1.8-1) ...
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Unpacking libasound2:amd64 (1.1.8-1) ...
7Progress: [ 14%] [########..................................................] 8Selecting previously unselected package libraw1394-11:amd64.
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Unpacking libraw1394-11:amd64 (2.1.2-1+b1) ...
Selecting previously unselected package libavc1394-0:amd64.
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Unpacking libavc1394-0:amd64 (0.5.4-5) ...
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7Progress: [ 15%] [########..................................................] 8Unpacking libass9:amd64 (1:0.14.0-2) ...
Selecting previously unselected package libbluray2:amd64.
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Unpacking libbluray2:amd64 (1:1.1.0-1) ...
Selecting previously unselected package libchromaprint1:amd64.
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Unpacking libchromaprint1:amd64 (1.4.3-3) ...
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7Progress: [ 16%] [#########.................................................] 8Unpacking libgme0:amd64 (0.6.2-1) ...
Selecting previously unselected package libmpg123-0:amd64.
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Unpacking libmpg123-0:amd64 (1.25.10-2) ...
Selecting previously unselected package libvorbisfile3:amd64.
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Unpacking libvorbisfile3:amd64 (1.3.6-2) ...
7Progress: [ 17%] [#########.................................................] 8Selecting previously unselected package libopenmpt0:amd64.
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Unpacking libopenmpt0:amd64 (0.4.3-1+deb10u1) ...
Selecting previously unselected package libssh-gcrypt-4:amd64.
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Unpacking libssh-gcrypt-4:amd64 (0.8.7-1+deb10u1) ...
Selecting previously unselected package libavformat58:amd64.
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7Progress: [ 18%] [##########................................................] 8Unpacking libavformat58:amd64 (7:4.1.6-1~deb10u1) ...
Selecting previously unselected package libbs2b0:amd64.
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Unpacking libbs2b0:amd64 (3.1.0+dfsg-2.2) ...
Selecting previously unselected package libflite1:amd64.
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Unpacking libflite1:amd64 (2.1-release-3) ...
7Progress: [ 19%] [###########...............................................] 8Selecting previously unselected package libserd-0-0:amd64.
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Unpacking libserd-0-0:amd64 (0.28.0~dfsg0-1) ...
Selecting previously unselected package libsord-0-0:amd64.
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7Progress: [ 20%] [###########...............................................] 8Unpacking libsratom-0-0:amd64 (0.6.0~dfsg0-1) ...
Selecting previously unselected package liblilv-0-0:amd64.
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Unpacking liblilv-0-0:amd64 (0.24.2~dfsg0-2) ...
Selecting previously unselected package libmysofa0:amd64.
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7Progress: [ 21%] [############..............................................] 8Selecting previously unselected package libpostproc55:amd64.
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78Collecting xlrd
Downloading xlrd-2.0.1-py2.py3-none-any.whl (96 kB)
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Installing collected packages: xlrd
Successfully installed xlrd-2.0.1
Collecting openpyxl
Downloading openpyxl-3.0.7-py2.py3-none-any.whl (243 kB)
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Collecting et-xmlfile
Downloading et_xmlfile-1.0.1.tar.gz (8.4 kB)
Building wheels for collected packages: et-xmlfile
Building wheel for et-xmlfile (setup.py) ... done
Created wheel for et-xmlfile: filename=et_xmlfile-1.0.1-py3-none-any.whl size=8913 sha256=d3a388add36bf37eb90188c41d35e362e31d44ba193cc308f380f66029c60b42
Stored in directory: /root/.cache/pip/wheels/e2/bd/55/048b4fd505716c4c298f42ee02dffd9496bb6d212b266c7f31
Successfully built et-xmlfile
Installing collected packages: et-xmlfile, openpyxl
Successfully installed et-xmlfile-1.0.1 openpyxl-3.0.7
count 100.000000
mean 0.071518
std 0.103884
min 0.000000
25% 0.021304
50% 0.052027
75% 0.091438
max 0.868421
Name: absfracdiff_grain, dtype: float64
/shared-libs/python3.7/py/lib/python3.7/site-packages/numpy/lib/function_base.py:2192: RuntimeWarning: invalid value encountered in ? (vectorized)
outputs = ufunc(*inputs)
count 100.000000
mean 0.283393
std 0.184866
min 0.000000
25% 0.133333
50% 0.250000
75% 0.428571
max 0.710526
Name: absfdiff_tube, dtype: float64
FileName Sample est_grain Total Pollen with Tube fracdiff_grain absfracdiff_grain est_tube fracdiff_tube absfdiff_tube
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2 Pure (66).tif 66 40 37 12 0.081081 0.081081 12 0.000000 0.000000
3 Pure (35).tif 35 46 44 23 0.045455 0.045455 14 -0.391304 0.391304
4 Pure (97).tif 97 54 51 18 0.058824 0.058824 15 -0.166667 0.166667
5 Pure (62).tif 62 19 19 12 0.000000 0.000000 9 -0.250000 0.250000
6 Pure (29).tif 29 71 60 29 0.183333 0.183333 9 -0.689655 0.689655
7 Pure (18).tif 18 73 71 30 0.028169 0.028169 21 -0.300000 0.300000
8 Pure (53).tif 53 16 16 8 0.000000 0.000000 9 0.125000 0.125000
9 Pure (3).tif 3 87 73 33 0.191781 0.191781 14 -0.575758 0.575758
10 Pure (31).tif 31 71 38 28 0.868421 0.868421 14 -0.500000 0.500000
11 Pure (93).tif 93 81 64 38 0.265625 0.265625 11 -0.710526 0.710526
12 Pure (47).tif 47 47 43 23 0.093023 0.093023 17 -0.260870 0.260870
13 Pure (76).tif 76 25 24 13 0.041667 0.041667 12 -0.076923 0.076923
14 Pure (14).tif 14 71 64 31 0.109375 0.109375 31 0.000000 0.000000
15 Pure (87).tif 87 43 43 25 0.000000 0.000000 12 -0.520000 0.520000
16 Pure (25).tif 25 31 31 15 0.000000 0.000000 18 0.200000 0.200000
17 Pure (39).tif 39 39 38 17 0.026316 0.026316 12 -0.294118 0.294118
18 Pure (72).tif 72 33 31 15 0.064516 0.064516 13 -0.133333 0.133333
19 Pure (43).tif 43 42 40 21 0.050000 0.050000 20 -0.047619 0.047619
20 Pure (83).tif 83 64 63 39 0.015873 0.015873 22 -0.435897 0.435897
21 Pure (21).tif 21 132 121 45 0.090909 0.090909 19 -0.577778 0.577778
22 Pure (10).tif 10 47 44 18 0.068182 0.068182 20 0.111111 0.111111
23 Pure (46).tif 46 47 46 27 0.021739 0.021739 21 -0.222222 0.222222
24 Pure (77).tif 77 32 32 14 0.000000 0.000000 12 -0.142857 0.142857
25 Pure (15).tif 15 37 35 15 0.057143 0.057143 13 -0.133333 0.133333
26 Pure (86).tif 86 48 42 12 0.142857 0.142857 11 -0.083333 0.083333
27 Pure (24).tif 24 37 35 19 0.057143 0.057143 16 -0.157895 0.157895
28 Pure (73).tif 73 50 46 31 0.086957 0.086957 20 -0.354839 0.354839
29 Pure (38).tif 38 52 47 20 0.106383 0.106383 16 -0.200000 0.200000
30 Pure (42).tif 42 90 74 11 0.216216 0.216216 7 -0.363636 0.363636
31 Pure (82).tif 82 65 45 31 0.444444 0.444444 10 -0.677419 0.677419
32 Pure (20).tif 20 43 44 21 -0.022727 0.022727 16 -0.238095 0.238095
33 Pure (11).tif 11 25 23 9 0.086957 0.086957 13 0.444444 0.444444
34 Pure (56).tif 56 29 28 13 0.035714 0.035714 10 -0.230769 0.230769
35 Pure (6).tif 6 88 82 15 0.073171 0.073171 17 0.133333 0.133333
36 Pure (67).tif 67 34 33 18 0.030303 0.030303 19 0.055556 0.055556
37 Pure (34).tif 34 52 52 12 0.000000 0.000000 15 0.250000 0.250000
38 Pure (96).tif 96 32 31 12 0.032258 0.032258 10 -0.166667 0.166667
39 Pure (28).tif 28 27 27 9 0.000000 0.000000 11 0.222222 0.222222
40 Pure (63).tif 63 34 34 16 0.000000 0.000000 15 -0.062500 0.062500
41 Pure (52).tif 52 22 22 7 0.000000 0.000000 4 -0.428571 0.428571
42 Pure (19).tif 19 19 19 3 0.000000 0.000000 3 0.000000 0.000000
43 Pure (2).tif 2 51 46 29 0.108696 0.108696 15 -0.482759 0.482759
44 Pure (30).tif 30 21 19 9 0.105263 0.105263 6 -0.333333 0.333333
45 Pure (92).tif 92 28 26 15 0.076923 0.076923 12 -0.200000 0.200000
46 Pure (44).tif 44 37 36 13 0.027778 0.027778 15 0.153846 0.153846
47 Pure (75).tif 75 43 42 26 0.023810 0.023810 10 -0.615385 0.615385
48 Pure (17).tif 17 51 46 27 0.108696 0.108696 20 -0.259259 0.259259
49 Pure (26).tif 26 69 68 43 0.014706 0.014706 23 -0.465116 0.465116
50 Pure (84).tif 84 43 39 21 0.102564 0.102564 16 -0.238095 0.238095
51 Pure (98).tif 98 51 50 29 0.020000 0.020000 24 -0.172414 0.172414
52 Pure (71).tif 71 44 42 23 0.047619 0.047619 14 -0.391304 0.391304
53 Pure (40).tif 40 57 53 12 0.075472 0.075472 15 0.250000 0.250000
54 Pure (69).tif 69 45 45 15 0.000000 0.000000 17 0.133333 0.133333
55 Pure (22).tif 22 50 47 28 0.063830 0.063830 12 -0.571429 0.571429
56 Pure (80).tif 80 42 42 14 0.000000 0.000000 8 -0.428571 0.428571
57 Pure (8).tif 8 83 73 36 0.136986 0.136986 12 -0.666667 0.666667
58 Pure (13).tif 13 38 35 16 0.085714 0.085714 8 -0.500000 0.500000
59 Pure (58).tif 58 66 57 8 0.157895 0.157895 9 0.125000 0.125000
60 Pure (4).tif 4 32 33 15 -0.030303 0.030303 19 0.266667 0.266667
61 Pure (54).tif 54 36 36 17 0.000000 0.000000 17 0.000000 0.000000
62 Pure (65).tif 65 48 48 15 0.000000 0.000000 8 -0.466667 0.466667
63 Pure (94).tif 94 24 23 8 0.043478 0.043478 6 -0.250000 0.250000
64 Pure (36).tif 36 71 66 31 0.075758 0.075758 21 -0.322581 0.322581
65 Pure (61).tif 61 25 25 8 0.000000 0.000000 9 0.125000 0.125000
66 Pure (88).tif 88 56 53 25 0.056604 0.056604 17 -0.320000 0.320000
67 Pure (50).tif 50 46 43 24 0.069767 0.069767 25 0.041667 0.041667
68 Pure (90).tif 90 44 42 20 0.047619 0.047619 19 -0.050000 0.050000
69 Pure (32).tif 32 42 41 21 0.024390 0.024390 13 -0.380952 0.380952
70 Pure (79).tif 79 47 46 36 0.021739 0.021739 17 -0.527778 0.527778
71 Pure (48).tif 48 41 40 20 0.025000 0.025000 17 -0.150000 0.150000
72 Pure (5).tif 5 68 64 37 0.062500 0.062500 20 -0.459459 0.459459
73 Pure (100).tif 100 50 45 15 0.111111 0.111111 11 -0.266667 0.266667
74 Pure (55).tif 55 26 25 19 0.040000 0.040000 12 -0.368421 0.368421
75 Pure (64).tif 64 71 64 23 0.109375 0.109375 19 -0.173913 0.173913
76 Pure (95).tif 95 63 62 32 0.016129 0.016129 20 -0.375000 0.375000
77 Pure (37).tif 37 33 34 17 -0.029412 0.029412 13 -0.235294 0.235294
78 Pure (60).tif 60 44 44 12 0.000000 0.000000 6 -0.500000 0.500000
79 Pure (89).tif 89 46 44 24 0.045455 0.045455 24 0.000000 0.000000
80 Pure (1).tif 1 56 55 17 0.018182 0.018182 16 -0.058824 0.058824
81 Pure (51).tif 51 65 56 28 0.160714 0.160714 17 -0.392857 0.392857
82 Pure (91).tif 91 67 61 28 0.098361 0.098361 15 -0.464286 0.464286
83 Pure (78).tif 78 25 24 8 0.041667 0.041667 9 0.125000 0.125000
84 Pure (33).tif 33 49 44 28 0.113636 0.113636 20 -0.285714 0.285714
85 Pure (49).tif 49 96 93 23 0.032258 0.032258 14 -0.391304 0.391304
86 Pure (45).tif 45 87 77 18 0.129870 0.129870 24 0.333333 0.333333
87 Pure (74).tif 74 46 44 18 0.045455 0.045455 28 0.555556 0.555556
88 Pure (16).tif 16 88 76 23 0.157895 0.157895 12 -0.478261 0.478261
89 Pure (27).tif 27 39 37 11 0.054054 0.054054 10 -0.090909 0.090909
90 Pure (85).tif 85 52 49 16 0.061224 0.061224 15 -0.062500 0.062500
91 Pure (99).tif 99 53 48 26 0.104167 0.104167 20 -0.230769 0.230769
92 Pure (70).tif 70 26 23 17 0.130435 0.130435 10 -0.411765 0.411765
93 Pure (41).tif 41 73 69 15 0.057971 0.057971 13 -0.133333 0.133333
94 Pure (23).tif 23 21 21 16 0.000000 0.000000 18 0.125000 0.125000
95 Pure (68).tif 68 77 76 44 0.013158 0.013158 18 -0.590909 0.590909
96 Pure (81).tif 81 43 40 19 0.075000 0.075000 14 -0.263158 0.263158
97 Pure (9).tif 9 47 44 21 0.068182 0.068182 12 -0.428571 0.428571
98 Pure (59).tif 59 35 33 19 0.060606 0.060606 17 -0.105263 0.105263
99 Pure (12).tif 12 30 30 21 0.000000 0.000000 21 0.000000 0.000000
0.25
0.05202702702702703