def test_csv_to_pd():
tf = tempfile.NamedTemporaryFile(suffix=".csv")
fid = open(tf.name, 'w')
fid.write(
"This file won't work. \n This file won't work. \n This file won't work."
)
fid.close()
stdout_ = sys.stdout
stream = StringIO()
sys.stdout = stream
test = ut.csv_to_pd(tf.name)
sys.stdout = stdout_
variable = stream.getvalue()
test_string = 'No data in csv file.\n'
assert (variable == test_string)
d = {
'Track_ID': [],
'Spot_ID': [],
'Frame': [],
'X': [],
'Y': [],
'Quality': [],
'SN_Ratio': [],
'Mean_Intensity': []
}
cols = [
'Track_ID', 'Spot_ID', 'Frame', 'X', 'Y', 'Quality', 'SN_Ratio',
'Mean_Intensity'
]
data = pd.DataFrame(data=d, index=[])
data = data[cols]
data = data.astype('float64')
pdt.assert_frame_equal(test, data)
tf = tempfile.NamedTemporaryFile(suffix=".csv")
fid = open(tf.name, 'w')
fid.write(
'Found 0 tracks.\nData starts here.\nTrack_ID,Spot_ID,Frame,X,Y,Quality,SN_Ratio,Mean_Intensity\n'
)
fid.close()
stdout_ = sys.stdout
stream = StringIO()
sys.stdout = stream
test = ut.csv_to_pd(tf.name)
sys.stdout = stdout_
variable = stream.getvalue()
test_string = ''
assert (variable == test_string)
pdt.assert_frame_equal(test, data)
def test_run_tracking():
tf = tempfile.NamedTemporaryFile(suffix='.csv')
ij.track('http://fiji.sc/samples/FakeTracks.tif', tf.name)
assert op.exists(tf.name)
df = csv_to_pd(tf.name)
assert df.shape == (84, 8)
def download_and_calc_MSDs(prefix):
import diff_classifier.aws as aws
import diff_classifier.utils as ut
import diff_classifier.msd as msd
import diff_classifier.features as ft
import os
import os.path as op
import numpy as np
import numpy.ma as ma
import pandas as pd
remote_folder = "01_18_Experiment/{}".format(prefix.split('_')[0])
local_folder = os.getcwd()
ires = 512
for row in range(0, 4):
for col in range(0, 4):
filename = "Traj_{}_{}_{}.csv".format(prefix, row, col)
to_download = remote_folder+'/'+filename
local_name = local_folder+'/'+filename
aws.download_s3(to_download, local_name)
if row==0 and col==0:
merged = msd.all_msds(ut.csv_to_pd(local_name))
else:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires*row
to_add['Y'] = to_add['Y'] + ires*col
to_add['Track_ID'] = to_add['Track_ID'] + max(merged['Track_ID'])
merged.append(msd.all_msds(to_add))
print('Successfully downloaded and calculated MSDs for {}_{}_{}'.format(prefix, row, col))
merged.to_csv('MSD_{}.csv'.format(prefix))
print('Saved MSDs as MSD_{}.csv'.format(prefix))
merged_ft = ft.calculate_features(merged)
merged_ft.to_csv('features_{}.csv'.format(prefix))
print('Saved features as features_{}.csv'.format(prefix))
def sensitivity_it(counter):
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import diff_classifier.aws as aws
import diff_classifier.utils as ut
import diff_classifier.msd as msd
import diff_classifier.features as ft
import diff_classifier.imagej as ij
import diff_classifier.heatmaps as hm
from scipy.spatial import Voronoi
import scipy.stats as stats
from shapely.geometry import Point
from shapely.geometry.polygon import Polygon
import matplotlib.cm as cm
import os
import os.path as op
import numpy as np
import numpy.ma as ma
import pandas as pd
import boto3
import itertools
#Sweep parameters
#----------------------------------
radius = [4.5, 6.0, 7.0]
do_median_filtering = [True, False]
quality = [1.5, 4.5, 8.5]
linking_max_distance = [6.0, 10.0, 15.0]
gap_closing_max_distance = [6.0, 10.0, 15.0]
max_frame_gap = [1, 2, 5]
track_displacement = [0.0, 10.0, 20.0]
sweep = [
radius, do_median_filtering, quality, linking_max_distance,
gap_closing_max_distance, max_frame_gap, track_displacement
]
all_params = list(itertools.product(*sweep))
#Variable prep
#----------------------------------
s3 = boto3.client('s3')
folder = '01_18_Experiment'
s_folder = '{}/sensitivity'.format(folder)
local_folder = '.'
prefix = "P1_S1_R_0001_2_2"
name = "{}.tif".format(prefix)
local_im = op.join(local_folder, name)
aws.download_s3(
'{}/{}/{}.tif'.format(folder,
prefix.split('_')[0], prefix),
'{}.tif'.format(prefix))
outputs = np.zeros((len(all_params), len(all_params[0]) + 2))
#Tracking and calculations
#------------------------------------
params = all_params[counter]
outfile = 'Traj_{}_{}.csv'.format(name.split('.')[0], counter)
msd_file = 'msd_{}_{}.csv'.format(name.split('.')[0], counter)
geo_file = 'geomean_{}_{}.csv'.format(name.split('.')[0], counter)
geoS_file = 'geoSEM_{}_{}.csv'.format(name.split('.')[0], counter)
msd_image = 'msds_{}_{}.png'.format(name.split('.')[0], counter)
iter_name = "{}_{}".format(prefix, counter)
ij.track(local_im,
outfile,
template=None,
fiji_bin=None,
radius=params[0],
threshold=0.,
do_median_filtering=params[1],
quality=params[2],
x=511,
y=511,
ylo=1,
median_intensity=300.0,
snr=0.0,
linking_max_distance=params[3],
gap_closing_max_distance=params[4],
max_frame_gap=params[5],
track_displacement=params[6])
traj = ut.csv_to_pd(outfile)
msds = msd.all_msds2(traj, frames=651)
msds.to_csv(msd_file)
gmean1, gSEM1 = hm.plot_individual_msds(iter_name, alpha=0.05)
np.savetxt(geo_file, gmean1, delimiter=",")
np.savetxt(geoS_file, gSEM1, delimiter=",")
aws.upload_s3(outfile, '{}/{}'.format(s_folder, outfile))
aws.upload_s3(msd_file, '{}/{}'.format(s_folder, msd_file))
aws.upload_s3(geo_file, '{}/{}'.format(s_folder, geo_file))
aws.upload_s3(geoS_file, '{}/{}'.format(s_folder, geoS_file))
aws.upload_s3(msd_image, '{}/{}'.format(s_folder, msd_image))
print('Successful parameter calculations for {}'.format(iter_name))
def assemble_msds(prefix, remote_folder, bucket,
ires=(512, 512), frames=651):
'''Calculates MSDs and features from input trajectory files
A function based on msd.all_msds2 and features.calculate_features, creates
msd and feature csv files from input trajectory files and uploads to S3.
Designed to work with Cloudknot for parallelizable workflows. Typically,
this function is used in conjunction with kn.split and kn.tracking for an
entire workflow.
prefix : string
Prefix (everything except file extension and folder name) of image file
to be tracked. Must be available on S3.
remote_folder : string
Folder name where file is contained on S3 in the bucket specified by
'bucket'.
bucket : string
S3 bucket where file is contained.
ires : tuple of int
Resolution of split images. Really just a sanity check to make sure you
correctly splitting.
frames : int
Number of frames in input videos.
'''
import os
import boto3
import diff_classifier.aws as aws
import diff_classifier.msd as msd
import diff_classifier.features as ft
import diff_classifier.utils as ut
filename = '{}.tif'.format(prefix)
remote_name = remote_folder+'/'+filename
msd_file = 'msd_{}.csv'.format(prefix)
ft_file = 'features_{}.csv'.format(prefix)
s3 = boto3.client('s3')
# names = []
# for i in range(0, 4):
# for j in range(0, 4):
# names.append('{}_{}_{}.tif'.format(prefix, i, j))
all_objects = s3.list_objects(Bucket=bucket,
Prefix='{}/{}_'.format(remote_folder,
prefix))
names = []
rows = 0
cols = 0
for entry in all_objects['Contents']:
name = entry['Key'].split('/')[-1]
names.append(name)
row = int(name.split(prefix)[1].split('.')[0].split('_')[-2])
col = int(name.split(prefix)[1].split('.')[0].split('_')[-1])
if row > rows:
rows = row
if col > cols:
cols = col
rows = rows + 1
cols = cols + 1
counter = 0
for name in names:
row = int(name.split(prefix)[1].split('.')[0].split('_')[-2])
col = int(name.split(prefix)[1].split('.')[0].split('_')[-1])
filename = "Traj_{}_{}_{}.csv".format(prefix, row, col)
aws.download_s3(remote_folder+'/'+filename, filename,
bucket_name=bucket)
local_name = filename
if counter == 0:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires[0]*col
to_add['Y'] = ires[1] - to_add['Y'] + ires[1]*(rows-1-row)
merged = msd.all_msds2(to_add, frames=frames)
else:
if merged.shape[0] > 0:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires[0]*col
to_add['Y'] = ires[1] - to_add['Y'] + ires[1]*(rows-1-row)
to_add['Track_ID'] = to_add['Track_ID'
] + max(merged['Track_ID']) + 1
else:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires[0]*col
to_add['Y'] = ires[1] - to_add['Y'] + ires[1]*(rows-1-row)
to_add['Track_ID'] = to_add['Track_ID']
merged = merged.append(msd.all_msds2(to_add, frames=frames))
print('Done calculating MSDs for row {} and col {}'.format(row,
col))
counter = counter + 1
merged.to_csv(msd_file)
aws.upload_s3(msd_file, remote_folder+'/'+msd_file, bucket_name=bucket)
merged_ft = ft.calculate_features(merged)
merged_ft.to_csv(ft_file)
aws.upload_s3(ft_file, remote_folder+'/'+ft_file, bucket_name=bucket)
os.remove(ft_file)
os.remove(msd_file)
for name in names:
outfile = 'Traj_' + name.split('.')[0] + '.csv'
os.remove(outfile)
def download_split_track_msds(prefix):
"""
1. Checks to see if features file exists.
2. If not, checks to see if image partitioning has occured.
3. If yes, checks to see if tracking has occured.
4. Regardless, tracks, calculates MSDs and features.
"""
import matplotlib as mpl
mpl.use('Agg')
import diff_classifier.aws as aws
import diff_classifier.utils as ut
import diff_classifier.msd as msd
import diff_classifier.features as ft
import diff_classifier.imagej as ij
import diff_classifier.heatmaps as hm
from scipy.spatial import Voronoi
import scipy.stats as stats
from shapely.geometry import Point
from shapely.geometry.polygon import Polygon
import matplotlib.cm as cm
import os
import os.path as op
import numpy as np
import numpy.ma as ma
import pandas as pd
import boto3
#Splitting section
###############################################################################################
remote_folder = "01_18_Experiment/{}".format(prefix.split('_')[0])
local_folder = os.getcwd()
ires = 512
frames = 651
filename = '{}.tif'.format(prefix)
remote_name = remote_folder+'/'+filename
local_name = local_folder+'/'+filename
msd_file = 'msd_{}.csv'.format(prefix)
ft_file = 'features_{}.csv'.format(prefix)
s3 = boto3.client('s3')
names = []
for i in range(0, 4):
for j in range(0, 4):
names.append('{}_{}_{}.tif'.format(prefix, i, j))
try:
obj = s3.head_object(Bucket='ccurtis7.pup', Key=remote_folder+'/'+ft_file)
except:
try:
for name in names:
aws.download_s3(remote_folder+'/'+name, name)
except:
aws.download_s3(remote_name, local_name)
names = ij.partition_im(local_name)
for name in names:
aws.upload_s3(name, remote_folder+'/'+name)
print("Done with splitting. Should output file of name {}".format(remote_folder+'/'+name))
#Tracking section
################################################################################################
for name in names:
outfile = 'Traj_' + name.split('.')[0] + '.csv'
local_im = op.join(local_folder, name)
row = int(name.split('.')[0].split('_')[4])
col = int(name.split('.')[0].split('_')[5])
try:
aws.download_s3(remote_folder+'/'+outfile, outfile)
except:
test_intensity = ij.mean_intensity(local_im)
if test_intensity > 500:
quality = 245
else:
quality = 4.5
if row==3:
y = 485
else:
y = 511
ij.track(local_im, outfile, template=None, fiji_bin=None, radius=4.5, threshold=0.,
do_median_filtering=True, quality=quality, x=511, y=y, ylo=1, median_intensity=300.0, snr=0.0,
linking_max_distance=8.0, gap_closing_max_distance=10.0, max_frame_gap=2,
track_displacement=10.0)
aws.upload_s3(outfile, remote_folder+'/'+outfile)
print("Done with tracking. Should output file of name {}".format(remote_folder+'/'+outfile))
#MSD and features section
#################################################################################################
files_to_big = False
size_limit = 10
for name in names:
outfile = 'Traj_' + name.split('.')[0] + '.csv'
local_im = name
file_size_MB = op.getsize(local_im)/1000000
if file_size_MB > size_limit:
file_to_big = True
if files_to_big:
print('One or more of the {} trajectory files exceeds {}MB in size. Will not continue with MSD calculations.'.format(
prefix, size_limit))
else:
counter = 0
for name in names:
row = int(name.split('.')[0].split('_')[4])
col = int(name.split('.')[0].split('_')[5])
filename = "Traj_{}_{}_{}.csv".format(prefix, row, col)
local_name = local_folder+'/'+filename
if counter == 0:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires*col
to_add['Y'] = ires - to_add['Y'] + ires*(3-row)
merged = msd.all_msds2(to_add, frames=frames)
else:
if merged.shape[0] > 0:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires*col
to_add['Y'] = ires - to_add['Y'] + ires*(3-row)
to_add['Track_ID'] = to_add['Track_ID'] + max(merged['Track_ID']) + 1
else:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires*col
to_add['Y'] = ires - to_add['Y'] + ires*(3-row)
to_add['Track_ID'] = to_add['Track_ID']
merged = merged.append(msd.all_msds2(to_add, frames=frames))
print('Done calculating MSDs for row {} and col {}'.format(row, col))
counter = counter + 1
merged.to_csv(msd_file)
aws.upload_s3(msd_file, remote_folder+'/'+msd_file)
merged_ft = ft.calculate_features(merged)
merged_ft.to_csv(ft_file)
aws.upload_s3(ft_file, remote_folder+'/'+ft_file)
#Plots
features = ('AR', 'D_fit', 'alpha', 'MSD_ratio', 'Track_ID', 'X', 'Y', 'asymmetry1', 'asymmetry2', 'asymmetry3',
'boundedness', 'efficiency', 'elongation', 'fractal_dim', 'frames', 'kurtosis', 'straightness', 'trappedness')
vmin = (1.36, 0.015, 0.72, -0.09, 0, 0, 0, 0.5, 0.049, 0.089, 0.0069, 0.65, 0.26, 1.28, 0, 1.66, 0.087, -0.225)
vmax = (3.98, 2.6, 2.3, 0.015, max(merged_ft['Track_ID']), 2048, 2048, 0.99, 0.415, 0.53,
0.062, 3.44, 0.75, 1.79, 650, 3.33, 0.52, -0.208)
die = {'features': features,
'vmin': vmin,
'vmax': vmax}
di = pd.DataFrame(data=die)
for i in range(0, di.shape[0]):
hm.plot_heatmap(prefix, feature=di['features'][i], vmin=di['vmin'][i], vmax=di['vmax'][i])
hm.plot_scatterplot(prefix, feature=di['features'][i], vmin=di['vmin'][i], vmax=di['vmax'][i])
hm.plot_trajectories(prefix)
try:
hm.plot_histogram(prefix)
except ValueError:
print("Couldn't plot histogram.")
hm.plot_particles_in_frame(prefix)
gmean1, gSEM1 = hm.plot_individual_msds(prefix, alpha=0.05)
def assemble_msds(prefix,
remote_folder,
bucket='nancelab.publicfiles',
ires=(512, 512),
frames=651,
rows=4,
cols=4):
'''Calculates MSDs and features from input trajectory files
A function based on msd.all_msds2 and features.calculate_features, creates
msd and feature csv files from input trajectory files and uploads to S3.
prefix : string
Prefix (everything except file extension and folder name) of image file
to be tracked. Must be available on S3.
remote_folder : string
Folder name where file is contained on S3 in the bucket specified by
'bucket'.
bucket : string
S3 bucket where file is contained.
ires : tuple of int
Resolution of split images. Really just a sanity check to make sure you
correctly splitting.
frames : int
Number of frames in input videos.
rows : int
Number of rows to split image into.
cols : int
Number of columns to split image into.
'''
import os
import boto3
import diff_classifier.aws as aws
import diff_classifier.msd as msd
import diff_classifier.features as ft
import diff_classifier.utils as ut
filename = '{}.tif'.format(prefix)
remote_name = remote_folder + '/' + filename
msd_file = 'msd_{}.csv'.format(prefix)
ft_file = 'features_{}.csv'.format(prefix)
s3 = boto3.client('s3')
names = []
for i in range(0, 4):
for j in range(0, 4):
names.append('{}_{}_{}.tif'.format(prefix, i, j))
counter = 0
for name in names:
row = int(name.split(prefix)[1].split('.')[0].split('_')[1])
col = int(name.split(prefix)[1].split('.')[0].split('_')[2])
filename = "Traj_{}_{}_{}.csv".format(prefix, row, col)
aws.download_s3(remote_folder + '/' + filename,
filename,
bucket_name=bucket)
local_name = filename
if counter == 0:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires[0] * col
to_add['Y'] = ires[1] - to_add['Y'] + ires[1] * (rows - 1 - row)
merged = msd.all_msds2(to_add, frames=frames)
else:
if merged.shape[0] > 0:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires[0] * col
to_add['Y'] = ires[1] - to_add['Y'] + ires[1] * (rows - 1 -
row)
to_add['Track_ID'] = to_add['Track_ID'] + max(
merged['Track_ID']) + 1
else:
to_add = ut.csv_to_pd(local_name)
to_add['X'] = to_add['X'] + ires[0] * col
to_add['Y'] = ires[1] - to_add['Y'] + ires[1] * (rows - 1 -
row)
to_add['Track_ID'] = to_add['Track_ID']
merged = merged.append(msd.all_msds2(to_add, frames=frames))
print('Done calculating MSDs for row {} and col {}'.format(
row, col))
counter = counter + 1
merged.to_csv(msd_file)
aws.upload_s3(msd_file, remote_folder + '/' + msd_file, bucket_name=bucket)
merged_ft = ft.calculate_features(merged)
merged_ft.to_csv(ft_file)
aws.upload_s3(ft_file, remote_folder + '/' + ft_file, bucket_name=bucket)
os.remove(ft_file)
os.remove(msd_file)
for name in names:
outfile = 'Traj_' + name.split('.')[0] + '.csv'
os.remove(outfile)