def __init__(self, path):
self.path = path
self.config_file = ConfigMaker(self.path)
self.hsv_jpg_file = ""
self.mask_png_file = ""
self.seed_labels_jpg_file = ""
self.imposed_annotation_jpg_file = ""
self.original_image_jpg_file = ""
self.html_file = HtmlMaker(self.path)
self.image_name = ""
self.csv_string = ""
# imagename,NumberofPeas,MeanAreaPixels,EqdMeanPixels,meanperimeterPixels
self.numberofseeds = 0
self.area_sum = 0
self.area_mean = 0
self.eqd_sum = 0
self.eqd_mean = 0
self.perimeter_sum = 0
self.perimeter_mean = 0
self.sum_max_mins = 0
self.mean_max_mins = 0
self.csv_file = Parameters.results + "/tables/workfile.csv"
self.accession_workfile = ""
self.csv_string_list = []
self.pixels_per_cm = 0.0
class seed:
def __init__(self, path):
self.path = path
self.config_file = ConfigMaker(self.path)
self.hsv_jpg_file = ""
self.mask_png_file = ""
self.seed_labels_jpg_file = ""
self.imposed_annotation_jpg_file = ""
self.original_image_jpg_file = ""
self.html_file = HtmlMaker(self.path)
self.image_name = ""
self.csv_string = ""
# imagename,NumberofPeas,MeanAreaPixels,EqdMeanPixels,meanperimeterPixels
self.numberofseeds = 0
self.area_sum = 0
self.area_mean = 0
self.eqd_sum = 0
self.eqd_mean = 0
self.perimeter_sum = 0
self.perimeter_mean = 0
self.sum_max_mins = 0
self.mean_max_mins = 0
self.csv_file = Parameters.results + "/tables/workfile.csv"
self.accession_workfile = ""
self.csv_string_list = []
self.pixels_per_cm = 0.0
def seed_analyse(self):
self.extract_image_ruler()
self.pixels_per_cm = self.image_ruler.pixels_per_cm
image_path_list = self.path.split("/")
self.image_name = image_path_list[-1]
self.csv_string = self.image_name + "\t"
self.accession_workfile = Parameters.results + "/tables/" + self.image_name + "_workfile.csv"
img = cv2.imread(self.path)
# figure(figsize=(15,15))
hsv = cv2.cvtColor(img, cv2.COLOR_BGR2HSV)
print "Making hsv image."
self.hsv_jpg_file = Parameters.results + "/images/" + self.image_name + "_hsv.jpg"
cv2.imwrite(self.hsv_jpg_file, hsv)
self.config_file.hsv_output_config_file(self.hsv_jpg_file)
upper_green = np.array([35, 255, 255])
lower_green = np.array([10, 100, 20])
mask = cv2.inRange(hsv, lower_green, upper_green)
res = cv2.bitwise_and(hsv, hsv, mask=mask)
mask = cv2.bilateralFilter(mask, 15, 75, 75)
print "Applying green mask_png_file."
self.mask_png_file = Parameters.results + "/images/" + self.image_name + "_imagemask.png"
cv2.imwrite(self.mask_png_file, mask)
self.config_file.mask_output_config_file(self.mask_png_file)
labels = skimg.measure.label(mask)
len(labels)
print "Creating labels for seeds."
self.seed_labels_jpg_file = Parameters.results + "/images/" + self.image_name + "_labels.png"
cv2.imwrite(self.seed_labels_jpg_file, labels)
self.config_file.seed_labels_output_config_file(
self.seed_labels_jpg_file)
properties = skimg.measure.regionprops(labels)
print len(properties)
print "Showing original image."
self.original_image_jpg_file = Parameters.results + "/images/" + self.image_name + "_img.png"
cv2.imwrite(self.original_image_jpg_file, img)
plt.figure(figsize=(10, 10))
plt.imshow(img)
self.config_file.original_image_jpg_output_config_file(
self.original_image_jpg_file)
clean_obj = []
clean_obj_contours = [
] #not used, but gives the contour for each of the seeds and could be useful later.
max_mins_list = []
eccentricity_list = []
eccentricity_sum = 0.0
counter = 0
sum_max_min = 0
im = Image.open(self.path)
draw = ImageDraw.Draw(im)
for p in properties:
if p.area > 1000:
if p.perimeter / p.equivalent_diameter < 5 and p.perimeter / p.equivalent_diameter > 3:
eccentricity_list.append(p.eccentricity)
eccentricity_sum += p.eccentricity
plt.annotate("%d" % (p.area, ),
xy=(p.centroid[1], p.centroid[0]))
plt.plot(p.centroid[1], p.centroid[0], 'o')
clean_obj.append(p)
reference_image = io.imread(self.path)
pea_hsv = color.rgb2hsv(reference_image)
pea_hue = pea_hsv[:, :, 0]
blank_img = np.zeros((pea_hue.shape[0], pea_hue.shape[1]),
dtype=np.uint8)
leaf_tmp = blank_img.copy() # also another array of zeros
###########################################
#TESTING - ADDING CONTOURS
ref_coord = p.coords.astype(int)
for count, value in enumerate(p.coords):
leaf_tmp[value[0]][value[1]] = 255
#leaf_tmp[ref_coord[:, 0], ref_coord[:, 1]] = 255
tmp_path = Parameters.tmp_dir + "/" + self.image_name + ".__" + str(
counter) + ".jpg"
io.imsave(tmp_path, leaf_tmp)
counter += 1
contours = skimg.measure.find_contours(
leaf_tmp, 0.8, fully_connected='high')
contours.sort(lambda x, y: cmp(len(x), len(y)))
#print "AREA: ", p.area
#for n, contour in enumerate(contours):
# print "length Contour: ", len(contour)
#if len(contour) > 200:
contour = contours[-1]
clean_obj_contours.append(contour)
#print "length Contour: ", len(contour)
distances = []
for m, point in enumerate(contour):
tuple = (int(point[1]), int(point[0]))
im.putpixel(tuple, (0, 255, 0, 255))
distance = math.sqrt(
math.pow(tuple[0] - p.centroid[0], 2) +
math.pow(tuple[1] - p.centroid[1], 2))
distances.append(distance)
#maximums = seed.get_maximum_points_on_contour(distances, 10)
#minimus = seed.get_minimum_points_on_contour(distances, 10)
position = []
for i, value in enumerate(contour):
position.append(i)
yhat = savgol_filter(
distances, 67, 8,
mode="nearest") # window size 51, polynomial order 3
maximums = signal.argrelmax(np.asarray(yhat))
minimums = signal.argrelmin(np.asarray(yhat))
max_min = (len(maximums) + len(minimums))
sum_max_min += max_min
max_mins_list.append(max_min)
#print "len max: ", len(maximums)
#print "len max: ", len(minimums)
plt.figure(num=None,
figsize=(18, 18),
dpi=80,
facecolor='w',
edgecolor='k')
plt.subplot(211)
plt.plot(position, distances, 'y-')
plt.plot(position, yhat, 'g-')
plt.xlabel("position on contour")
plt.ylabel("distance from centroid")
plt.title("pea contour plot")
for m, value in enumerate(maximums[0]):
#print "value:",value
plt.plot(position[value], distances[value], 'ro')
x = int(contour[value][1])
y = int(contour[value][0])
r = 2
#im.putpixel(max, (0, 0, 255, 255))
draw.ellipse((x - r, y - r, x + r, y + r),
fill=(255, 0, 0, 255))
for m, value in enumerate(minimums[0]):
#print "value: ", value
plt.plot(position[value], distances[value], 'bo')
x = int(contour[value][1])
y = int(contour[value][0])
r = 2
#im.putpixel(max, (0, 0, 255, 255))
draw.ellipse((x - r, y - r, x + r, y + r),
fill=(0, 0, 255, 255))
plt.savefig(Parameters.tmp_dir + "/" + self.image_name +
".pea_plot." + str(counter) + ".png",
bbox_inches='tight')
draw.ellipse((p.centroid[1] - r, p.centroid[0] - r,
p.centroid[1] + r, p.centroid[0] + r),
fill=(255, 0, 0, 255))
if counter == 0:
return self.image_name + ",empty,,,,,,,,,\n"
self.mean_max_mins = sum_max_min / counter
im.save(Parameters.tmp_dir + "/" + self.image_name +
".with_contours.jpg")
plt.xlim((0, img.shape[1]))
plt.ylim((img.shape[0], 0))
print "Imposing annotation onto image."
self.imposed_annotation_jpg_file = Parameters.results + "/images/" + self.image_name + "_imposed.png"
plt.savefig(self.imposed_annotation_jpg_file, bbox_inches=None)
self.config_file.imposed_annotation_output_config_file(
self.imposed_annotation_jpg_file)
# Descriptive stats
self.numberofseeds = str(len(clean_obj))
# print "Number of peas found: \t%d" %(len(clean_obj), )
# print "Mean pea size: \t\t%.2f" %(np.array([p.area for p in clean_obj]).mean(), )
# print "Sd for mean pea size: \t%.2f" %(np.array([p.area for p in clean_obj]).std(), )
#
# print "The median is %f" % (np.median(np.array([p.area for p in clean_obj])))
# print "The maximum is %f" % (np.max(np.array([p.area for p in clean_obj])))
# print "The minimum is %f" % (np.min(np.array([p.area for p in clean_obj])))
# draw violin plot
rep_area = [p.area for p in clean_obj]
rep_eqd = [p.equivalent_diameter for p in clean_obj]
rep_perimeter = [p.perimeter for p in clean_obj]
rep_centroid = [p.centroid for p in clean_obj]
#####
self.html_file.accession_area_pixel_maker(rep_area, self.image_name)
self.html_file.accession_eqd_pixel_maker(rep_eqd, self.image_name)
self.html_file.accession_perimeter_pixel_maker(rep_perimeter,
self.image_name)
#####################
# Create averages for each
#####################
for i in rep_area:
self.area_sum = float(self.area_sum) + float(i)
self.area_mean = self.area_sum / float(self.numberofseeds)
self.area_mean = str(self.area_mean)
for i in rep_eqd:
self.eqd_sum = float(self.eqd_sum) + float(i)
self.eqd_mean = self.eqd_sum / float(self.numberofseeds)
self.eqd_mean = str(self.eqd_mean)
for i in rep_perimeter:
self.perimeter_sum = float(self.perimeter_sum) + float(i)
self.perimeter_mean = self.perimeter_sum / float(self.numberofseeds)
self.perimeter_mean = str(self.perimeter_mean)
#####################
# create a table (1 accession, all seeds)
#####################
workfile = open(self.accession_workfile, "w")
workfile.write(
"Perimeter,Area,Equivalent Diameter,max_mins, eccentricity\n")
for i in range(len(clean_obj)):
seed_string = str(rep_perimeter[i]) + "," + str(
rep_area[i]) + "," + str(rep_eqd[i]) + "," + str(
max_mins_list[i]) + "," + str(eccentricity_list[i])
workfile.write(seed_string)
workfile.write("\n")
workfile.close()
df = pd.read_csv(self.accession_workfile, sep=",")
df.index = np.arange(1, len(df) + 1)
seed_table = df.to_html(justify='left')
list_seed_table = seed_table.split('\n')
del list_seed_table[0]
del list_seed_table[-1]
seed_table = "\n".join(list_seed_table)
self.html_file.accession_seed_table_file_maker(seed_table,
self.image_name)
self.html_file.accession_method_html_maker(
self.original_image_jpg_file, self.hsv_jpg_file,
self.mask_png_file, self.seed_labels_jpg_file,
self.imposed_annotation_jpg_file, self.image_name)
print "Printing csv string for this accession: ", self.image_name
one_over_pix_per_cm = float(1.0 / float(self.pixels_per_cm))
area_mean_cm = float(
self.area_mean) * one_over_pix_per_cm * one_over_pix_per_cm
eqd_mean_cm = float(self.eqd_mean) / float(self.pixels_per_cm)
perimeter_mean_cm = float(self.perimeter_mean) / float(
self.pixels_per_cm)
ecc_mean = float(eccentricity_sum) / counter
self.csv_string = self.image_name + "," + \
self.numberofseeds + "," + \
self.area_mean + "," + \
self.eqd_mean + "," + \
self.perimeter_mean + "," + \
str(self.mean_max_mins) + "," + \
str(self.pixels_per_cm) + "," + \
str(area_mean_cm) + "," + \
str(eqd_mean_cm) + "," + \
str(perimeter_mean_cm) + "," + \
str(ecc_mean) + "\n"
return self.csv_string
def extract_image_ruler(self):
print "extract_image_ruler: ", self.path
reference_image = io.imread(self.path)
resized_image_ruler = rescale(reference_image, 0.5,
mode='constant') # 50% more pixels
image_path_list = self.path.split("/")
image_name = image_path_list[-1]
dst = Parameters.tmp_dir + "/" + image_name
io.imsave(dst, resized_image_ruler)
self.image_ruler = RulerMeasure(dst, self.config_file)
# add success for this process to the config
#self.config_file.resizedforruler_output_config_file(self.path + ".resizedforruler.jpg")
self.image_ruler.process_ruler()
def __init__(self):
self.config_file = ConfigMaker(Parameters.results +
"/summary_output.config")
class HtmlMaker:
def __init__(self, config):
self.images = []
self.config_file = ConfigMaker(Parameters.results +
"/summary_output.config")
def make_html(self, out_dir, images):
""" Making SUMMARY Table """
# open tsv file
f_tsv = open(Parameters.results + '/tables/workfile.tsv', "r")
# make new html
f = open(Parameters.results + "/html/html_summary_table.html", 'w')
# read tsv as thml
tsv_data_to_html = pd.read_table(f_tsv, "\t")
html_table = tsv_data_to_html.to_html()
my_html_table_list = html_table.split("\n")
# substitute lines in table
table_index = my_html_table_list.index(
"<table border=\"1\" class=\"dataframe\">")
my_html_table_list[
table_index] = "<table class=\"table table-striped results\">"
header_string = "<tr style=\"text-align: right;\">"
sub_str = [s for s in my_html_table_list if header_string in s]
new_sub_str = str(sub_str[0])
table_index = my_html_table_list.index(new_sub_str)
my_html_table_list[table_index] = "<tr style=\"text-align: left;\">"
header_string = "<th>Area_cm2</th>"
sub_str = [s for s in my_html_table_list if header_string in s]
new_sub_str = str(sub_str[0])
table_index = my_html_table_list.index(new_sub_str)
my_html_table_list[table_index] = "<th>Area cm<sup>2</sup></th>"
header_string = "<th>Length_cm</th>"
sub_str = [s for s in my_html_table_list if header_string in s]
new_sub_str = str(sub_str[0])
table_index = my_html_table_list.index(new_sub_str)
my_html_table_list[table_index] = "<th>Length cm</th>"
header_string = "<th>Width_cm</th>"
sub_str = [s for s in my_html_table_list if header_string in s]
new_sub_str = str(sub_str[0])
table_index = my_html_table_list.index(new_sub_str)
my_html_table_list[table_index] = "<th>Width cm</th>"
header_string = "<th>Perimeter_cm</th>"
sub_str = [s for s in my_html_table_list if header_string in s]
new_sub_str = str(sub_str[0])
table_index = my_html_table_list.index(new_sub_str)
my_html_table_list[table_index] = "<th>Perimeter cm</th>"
joined_table = '\n'.join(my_html_table_list)
# open index html
# my_html_test_doc = []
f2 = open("../resources/html/index_summary.html", "r")
my_html_test_doc = f2.read().split('\n')
# substitute lines in html doc
html_index = my_html_test_doc.index("THIS IS TABLE")
my_html_test_doc[html_index] = joined_table
html_index = my_html_test_doc.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc[html_index] = bootstrap_string
html_index = my_html_test_doc.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc)
f.write(str_for_html)
# close
f.close()
f2.close()
# f_tsv.close()
# open
filename = 'file://' + Parameters.results + "/html/html_summary_table.html"
# add success for this process to the config
self.config_file.html_summary_output_config_file(
Parameters.results + "/html/html_summary_table.html")
""" Making Summary Plots Pixels """
# TODO: MAKE PATHS RELEATIVE!!!!!!
f_plot_pixel = open(
Parameters.results +
'/html/html_summary_plot_pixels_morphological.html', 'w')
my_html_test_doc_plot_pixels = []
f1_p = open(
'../resources/html/index_plot_leaf_morphological_pixels.html', "r")
my_html_test_doc_plot_pixels = f1_p.read().split('\n')
# print tsv_data_to_html
# violin plot data entry PIXELS
# length
length = tsv_data_to_html["Length"].tolist()
string_length_array = "var x14=[length]"
html_index = my_html_test_doc_plot_pixels.index(string_length_array)
my_html_test_doc_plot_pixels[html_index] = "var x14=%s" % length
#####################
print "Adding length pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Major axis length (length) in Pixels")
plt.boxplot(length, 0, 'rs', 0)
boxplot_path_length_pixels = Parameters.results + "/images/plot_length_pixels.png"
savefig(boxplot_path_length_pixels)
self.config_file.length_pixels_boxplot_output_config_file(
boxplot_path_length_pixels)
#####################
# width
width = tsv_data_to_html["Width"].tolist()
string_width_array = "var x13=[width]"
html_index = my_html_test_doc_plot_pixels.index(string_width_array)
my_html_test_doc_plot_pixels[html_index] = "var x13=%s" % width
#####################
print "Adding width pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Minor axis length (width) in Pixels")
plt.boxplot(width, 0, 'rs', 0)
boxplot_path_width_pixels = Parameters.results + "/images/plot_width_pixels.png"
savefig(boxplot_path_width_pixels)
self.config_file.width_pixels_boxplot_output_config_file(
boxplot_path_width_pixels)
#####################
# area
area = tsv_data_to_html["Area"].tolist()
string_area_array = "var x12=[area]"
html_index = my_html_test_doc_plot_pixels.index(string_area_array)
my_html_test_doc_plot_pixels[html_index] = "var x12=%s" % area
#####################
print "Adding area pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Area in Pixels")
plt.boxplot(area, 0, 'rs', 0)
boxplot_path_area_pixels = Parameters.results + "/images/plot_area_pixels.png"
savefig(boxplot_path_area_pixels)
self.config_file.area_pixels_boxplot_output_config_file(
boxplot_path_area_pixels)
#####################
# perimeter
perimeter = tsv_data_to_html["Perimeter"].tolist()
string_perimeter_array = "var x11=[perimeter]"
html_index = my_html_test_doc_plot_pixels.index(string_perimeter_array)
my_html_test_doc_plot_pixels[html_index] = "var x11=%s" % perimeter
#####################
print "Adding perimeter pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Perimeter in Pixels")
plt.boxplot(perimeter, 0, 'rs', 0)
boxplot_path_perimeter_pixels = Parameters.results + "/images/plot_perimeter_pixels.png"
savefig(boxplot_path_perimeter_pixels)
self.config_file.perimeter_pixels_boxplot_output_config_file(
boxplot_path_perimeter_pixels)
#####################
html_index = my_html_test_doc_plot_pixels.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_pixels[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_pixels.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_pixels[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_pixels)
f_plot_pixel.write(str_for_html)
f_plot_pixel.close()
f1_p.close()
filename_plot = 'file://' + Parameters.results + '/html/html_summary_plot_pixels_morphological.html'
# add success for this process to the config
self.config_file.html_plot_pixels_morphological_output_config_file(
Parameters.results +
'/html/html_summary_plot_pixels_morphological.html')
f_plot_pixel = open(
Parameters.results + '/html/html_summary_plot_pixels_eqs.html',
'w')
my_html_test_doc_plot_pixels = []
f2_p = open('../resources/html/index_plot_leaf_eq_pixels.html', "r")
my_html_test_doc_plot_pixels = f2_p.read().split('\n')
equivalent_diameter = tsv_data_to_html["Equivalent Diameter"].tolist()
string_equivalentdiameter_array = "var x9=[equivalentdiameter]"
html_index = my_html_test_doc_plot_pixels.index(
string_equivalentdiameter_array)
my_html_test_doc_plot_pixels[
html_index] = "var x9=%s" % equivalent_diameter
html_index = my_html_test_doc_plot_pixels.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_pixels[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_pixels.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_pixels[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_pixels)
f_plot_pixel.write(str_for_html)
f_plot_pixel.close()
f2.close()
filename_plot = 'file://' + Parameters.results + '/html/html_summary_plot_pixels_eqs.html'
# add success for this process to the config
self.config_file.html_summary_plot_pixels_eqs_output_config_file(
Parameters.results + '/html/html_summary_plot_pixels_eqs.html')
#####################
print "Adding equivalent diameter pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Equivalent Diameter in Pixels")
plt.boxplot(equivalent_diameter, 0, 'rs', 0)
boxplot_path_eqd_pixels = Parameters.results + "/images/plot_eqd_pixels.png"
savefig(boxplot_path_eqd_pixels)
self.config_file.perimeter_pixels_boxplot_output_config_file(
boxplot_path_eqd_pixels)
#####################
""" Making Summary plot CM """
###########
# CM PLOTS
f_plot_leaf_morphological_cm = open(
Parameters.results +
'/html/html_summary_plot_leaf_morphological_cm.html', 'w')
f3 = open('../resources/html/index_plot_leaf_morphological_cm.html',
"r")
my_html_test_doc_plot_cm = f3.read().split('\n')
# violin plot data entry CM
# length
length_cm = tsv_data_to_html["Length_cm"].tolist()
string_length_array = "var x14=[length]"
html_index = my_html_test_doc_plot_cm.index(string_length_array)
my_html_test_doc_plot_cm[html_index] = "var x14=%s" % length_cm
#####################
print "Adding length cm boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Major Axis Length (length) in Centimeters")
plt.boxplot(length_cm, 0, 'rs', 0)
boxplot_path_length_cm = Parameters.results + "/images/plot_length_cm.png"
savefig(boxplot_path_length_cm)
self.config_file.length_cm_boxplot_output_config_file(
boxplot_path_length_cm)
#####################
# width
width_cm = tsv_data_to_html["Width_cm"].tolist()
string_width_array = "var x13=[width]"
html_index = my_html_test_doc_plot_cm.index(string_width_array)
my_html_test_doc_plot_cm[html_index] = "var x13=%s" % width_cm
#####################
print "Adding width cm boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Minor Axis Length (Width) in Centimeters")
plt.boxplot(width_cm, 0, 'rs', 0)
boxplot_path_width_cm = Parameters.results + "/images/plot_width_cm.png"
savefig(boxplot_path_width_cm)
self.config_file.width_cm_boxplot_output_config_file(
boxplot_path_width_cm)
#####################
# area
area_cm = tsv_data_to_html["Area_cm2"].tolist()
string_area_array = "var x12=[area]"
html_index = my_html_test_doc_plot_cm.index(string_area_array)
my_html_test_doc_plot_cm[html_index] = "var x12=%s" % area_cm
#####################
print "Adding area cm boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Area in Centimeters")
plt.boxplot(area_cm, 0, 'rs', 0)
boxplot_path_area_cm = Parameters.results + "/images/plot_area_cm.png"
savefig(boxplot_path_area_cm)
self.config_file.area_cm_boxplot_output_config_file(
boxplot_path_area_cm)
#####################
# perimeter
perimeter_cm = tsv_data_to_html["Perimeter_cm"].tolist()
string_perimeter_array = "var x11=[perimeter]"
html_index = my_html_test_doc_plot_cm.index(string_perimeter_array)
my_html_test_doc_plot_cm[html_index] = "var x11=%s" % perimeter_cm
#####################
print "Adding perimeter cm boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Perimeter in Centimeters")
plt.boxplot(perimeter_cm, 0, 'rs', 0)
boxplot_path_perimeter_cm = Parameters.results + "/images/plot_perimeter_cm.png"
savefig(boxplot_path_perimeter_cm)
self.config_file.perimeter_cm_boxplot_output_config_file(
boxplot_path_perimeter_cm)
#####################
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_cm)
f_plot_leaf_morphological_cm.write(str_for_html)
f_plot_leaf_morphological_cm.close()
f3.close()
filename_plot_cm = 'file://' + Parameters.results + '/html/html_summary_plot_leaf_morphological_cm.html'
# add success for this process to the config
self.config_file.html_summary_plot_leaf_morphological_cm_output_config_file(
Parameters.results +
'/html/html_summary_plot_leaf_morphological_cm.html')
# TODO: make pixel morphological and eqd
# TODO: add label to the end of this all files
##############################
f_plot_leaf_teeth = open(
Parameters.results + '/html/html_summary_plot_leaf_teeth.html',
'w')
f4 = open('../resources/html/index_plot_leaf_teeth.html', "r")
my_html_test_doc_plot_cm = f4.read().split('\n')
number_of_teeth = tsv_data_to_html["NumberofTeeth"].tolist()
string_number_of_teeth_array = "var x10=[numberofteeth]"
html_index = my_html_test_doc_plot_cm.index(
string_number_of_teeth_array)
my_html_test_doc_plot_cm[html_index] = "var x10=%s" % number_of_teeth
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_cm)
f_plot_leaf_teeth.write(str_for_html)
f_plot_leaf_teeth.close()
f4.close()
filename_plot_cm = 'file://' + Parameters.results + '/html/html_summary_plot_leaf_teeth.html'
# add success for this process to the config
self.config_file.html_summary_plot_leaf_teeth_output_config_file(
Parameters.results + '/html/html_summary_plot_leaf_teeth.html')
#####################
print "Adding number of teeth boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Number of Teeth")
plt.boxplot(number_of_teeth, 0, 'rs', 0)
boxplot_path_number_of_teeth = Parameters.results + "/images/plot_number_of_teeth.png"
savefig(boxplot_path_number_of_teeth)
self.config_file.number_of_teeth_boxplot_output_config_file(
boxplot_path_number_of_teeth)
#####################
# shape descriptors
f_plot_leaf_shape = open(
Parameters.results + '/html/html_summary_plot_leaf_shape.html',
'w')
f5 = open('../resources/html/index_plot_leaf_shape.html', "r")
my_html_test_doc_plot_cm = f5.read().split('\n')
aspect_ratio = tsv_data_to_html["AspectRatio"].tolist()
string_aspect_ratio_array = "var x0=[aspectratio]"
html_index = my_html_test_doc_plot_cm.index(string_aspect_ratio_array)
my_html_test_doc_plot_cm[html_index] = "var x0=%s" % aspect_ratio
#####################
print "Adding aspect ratio boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Aspect Ratio")
plt.boxplot(aspect_ratio, 0, 'rs', 0)
boxplot_path_aspect_ratio = Parameters.results + "/images/plot_aspect_ratio.png"
savefig(boxplot_path_aspect_ratio)
self.config_file.aspect_ratio_boxplot_output_config_file(
boxplot_path_aspect_ratio)
#####################
perimeter_ratio_of_length = tsv_data_to_html[
"Perimeter Ratio of Length"].tolist()
string_perimeter_ratio_of_length_array = "var x4=[perimeterratiooflength]"
html_index = my_html_test_doc_plot_cm.index(
string_perimeter_ratio_of_length_array)
my_html_test_doc_plot_cm[
html_index] = "var x4=%s" % perimeter_ratio_of_length
#####################
print "Adding perimeter_ratio_of_length boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Perimeter Ratio of Length")
plt.boxplot(perimeter_ratio_of_length, 0, 'rs', 0)
boxplot_path_perimeter_ratio_of_length = Parameters.results + "/images/plot_perimeter_ratio_of_length.png"
savefig(boxplot_path_perimeter_ratio_of_length)
self.config_file.perimeter_ratio_of_length_boxplot_output_config_file(
boxplot_path_perimeter_ratio_of_length)
#####################
perimeter_ratio_of_length_and_width = tsv_data_to_html[
"Perimeter Ratio of Length and Width"].tolist()
string_perimeter_ratio_of_length_and_width_array = "var x5=[perimeterratiooflengthandwidth]"
html_index = my_html_test_doc_plot_cm.index(
string_perimeter_ratio_of_length_and_width_array)
my_html_test_doc_plot_cm[
html_index] = "var x5=%s" % perimeter_ratio_of_length_and_width
#####################
print "Adding perimeter_ratio_of_length_and_width boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Perimeter Ratio of Length and Width")
plt.boxplot(perimeter_ratio_of_length_and_width, 0, 'rs', 0)
boxplot_path_perimeter_ratio_of_length_and_withd = Parameters.results + "/images/plot_perimeter_ratio_of_length_and_width.png"
savefig(boxplot_path_perimeter_ratio_of_length_and_withd)
self.config_file.perimeter_ratio_of_length_and_width_boxplot_output_config_file(
boxplot_path_perimeter_ratio_of_length_and_withd)
#####################
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_cm)
f_plot_leaf_shape.write(str_for_html)
f_plot_leaf_shape.close()
f5.close()
filename_plot_cm = 'file://' + Parameters.results + '/html/html_summary_plot_leaf_shape.html'
# add success for this process to the config
self.config_file.html_summary_plot_leaf_shape_output_config_file(
Parameters.results + '/html/html_summary_plot_leaf_shape.html')
# shapedescriptors2
f_plot_leaf_shape2 = open(
Parameters.results + '/html/html_summary_plot_leaf_shape2.html',
'w')
f6 = open('../resources/html/index_plot_leaf_shape2.html', "r")
my_html_test_doc_plot_cm = f6.read().split('\n')
roundness = tsv_data_to_html["Roundness"].tolist()
string_roundness_array = "var x1=[roundness]"
html_index = my_html_test_doc_plot_cm.index(string_roundness_array)
my_html_test_doc_plot_cm[html_index] = "var x1=%s" % roundness
#####################
print "Adding roundness boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Roundness")
plt.boxplot(roundness, 0, 'rs', 0)
boxplot_path_roundness = Parameters.results + "/images/plot_roundness.png"
savefig(boxplot_path_roundness)
self.config_file.roundness_boxplot_output_config_file(
boxplot_path_roundness)
#####################
rectangularity = tsv_data_to_html["Rectangularity"].tolist()
string_rectangularity_array = "var x3=[rectangularity]"
html_index = my_html_test_doc_plot_cm.index(
string_rectangularity_array)
my_html_test_doc_plot_cm[html_index] = "var x3=%s" % rectangularity
#####################
print "Adding rectangularity boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Rectangularity")
plt.boxplot(rectangularity, 0, 'rs', 0)
boxplot_path_rectangularity = Parameters.results + "/images/plot_rectangularity.png"
savefig(boxplot_path_rectangularity)
self.config_file.rectangularity_boxplot_output_config_file(
boxplot_path_rectangularity)
#####################
perimeter_convexity = tsv_data_to_html["Perimeter Convexity"].tolist()
string_perimeter_convexity_array = "var x6=[perimeterconvexity]"
html_index = my_html_test_doc_plot_cm.index(
string_perimeter_convexity_array)
my_html_test_doc_plot_cm[
html_index] = "var x6=%s" % perimeter_convexity
#####################
print "Adding perimeter convexity boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Perimeter Convexity")
plt.boxplot(perimeter_convexity, 0, 'rs', 0)
boxplot_path_perimeter_convexity = Parameters.results + "/images/plot_perimeter_convexity.png"
savefig(boxplot_path_perimeter_convexity)
self.config_file.perimeter_convexity_boxplot_output_config_file(
boxplot_path_perimeter_convexity)
#####################
area_convexity = tsv_data_to_html["Area Convexity"].tolist()
string_area_convexity_array = "var x7=[areaconvexity]"
html_index = my_html_test_doc_plot_cm.index(
string_area_convexity_array)
my_html_test_doc_plot_cm[html_index] = "var x7=%s" % area_convexity
#####################
print "Adding area convexity boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Area Convexity")
plt.boxplot(area_convexity, 0, 'rs', 0)
boxplot_path_area_convexity = Parameters.results + "/images/plot_area_convexity.png"
savefig(boxplot_path_area_convexity)
self.config_file.area_convexity_boxplot_output_config_file(
boxplot_path_area_convexity)
#####################
area_ratio_of_convexity = tsv_data_to_html[
"Area Ratio of Convexity"].tolist()
string_area_ratio_of_convexity_array = "var x8=[arearatioofconvexity]"
html_index = my_html_test_doc_plot_cm.index(
string_area_ratio_of_convexity_array)
my_html_test_doc_plot_cm[
html_index] = "var x8=%s" % area_ratio_of_convexity
#####################
print "Adding area ratio of convexity boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Area Ratio of Convexity")
plt.boxplot(area_ratio_of_convexity, 0, 'rs', 0)
boxplot_path_area_ratio_of_convexity = Parameters.results + "/images/plot_area_ratio_of_convexity.png"
savefig(boxplot_path_area_ratio_of_convexity)
self.config_file.area_ratio_of_convexity_boxplot_output_config_file(
boxplot_path_area_ratio_of_convexity)
#####################
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_cm)
f_plot_leaf_shape2.write(str_for_html)
f_plot_leaf_shape2.close()
f6.close()
filename_plot_cm = 'file://' + Parameters.results + '/html/html_summary_plot_leaf_shape2.html'
# add success for this process to the config
self.config_file.html_summary_plot_leaf_shape2_output_config_file(
Parameters.results + '/html/html_summary_plot_leaf_shape2.html')
# compactness
f_plot_leaf_compactness = open(
Parameters.results +
'/html/html_summary_plot_leaf_compactness.html', 'w')
f7 = open('../resources/html/index_plot_leaf_compactness.html', "r")
my_html_test_doc_plot_cm = f7.read().split('\n')
compactness = tsv_data_to_html["Compactness"].tolist()
string_compactness_array = "var x2=[compactness]"
html_index = my_html_test_doc_plot_cm.index(string_compactness_array)
my_html_test_doc_plot_cm[html_index] = "var x2=%s" % compactness
#####################
print "Adding compactness boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Compactness")
plt.boxplot(compactness, 0, 'rs', 0)
boxplot_path_compactness = Parameters.results + "/images/plot_compactness.png"
savefig(boxplot_path_compactness)
self.config_file.compactness_boxplot_output_config_file(
boxplot_path_compactness)
#####################
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_cm)
f_plot_leaf_compactness.write(str_for_html)
f_plot_leaf_compactness.close()
f7.close()
filename_plot_cm = 'file://' + Parameters.results + '/html/html_summary_plot_leaf_compactness.html'
# add success for this process to the config
self.config_file.html_summary_plot_leaf_compactness_output_config_file(
Parameters.results +
'/html/html_summary_plot_leaf_compactness.html')
# equivalent diameter in cm
f_plot_leaf_eqd_cm = open(
Parameters.results + '/html/html_summary_plot_leaf_eqd_cm.html',
'w')
f8 = open('../resources/html/index_plot_leaf_eqd_cm.html', "r")
my_html_test_doc_plot_cm = f8.read().split('\n')
equivalent_diameter = tsv_data_to_html[
"Equivalent Diameter cm"].tolist()
string_equivalent_diameter_array = "var x9=[equivalentdiameter]"
html_index = my_html_test_doc_plot_cm.index(
string_equivalent_diameter_array)
my_html_test_doc_plot_cm[
html_index] = "var x9=%s" % equivalent_diameter
#####################
print "Adding equivalent diameter cm boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Equivalent Diameter in cm")
plt.boxplot(equivalent_diameter, 0, 'rs', 0)
boxplot_path_eqd_cm = Parameters.results + "/images/plot_eqd_cm.png"
savefig(boxplot_path_eqd_cm)
self.config_file.eqd_cm_boxplot_output_config_file(boxplot_path_eqd_cm)
#####################
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"bootstrap.min.css\" rel=\"stylesheet\">")
bootstrap_string = "<link href=\"" + Parameters.resources + "/css/bootstrap.min.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = bootstrap_string
html_index = my_html_test_doc_plot_cm.index(
"<link href=\"dashboard.css\" rel=\"stylesheet\">")
dashboard_string = "<link href=\"" + Parameters.resources + "/css/dashboard.css\" rel=\"stylesheet\">"
my_html_test_doc_plot_cm[html_index] = dashboard_string
str_for_html = "\n".join(my_html_test_doc_plot_cm)
f_plot_leaf_eqd_cm.write(str_for_html)
f_plot_leaf_eqd_cm.close()
f8.close()
filename_plot_cm = 'file://' + Parameters.results + '/html/html_summary_plot_leaf_eqd_cm.html'
# add success for this process to the config
self.config_file.html_summary_plot_leaf_eqd_cm_output_config_file(
Parameters.results + '/html/html_summary_plot_leaf_eqd_cm.html')
boxplot_pixels = open(
Parameters.results + '/html/html_boxplot_pixels.html', 'w')
boxplot_template = open(
Parameters.resources + '/html/boxplot_template.html', "r")
my_html_boxplot_pixels = boxplot_template.read().split('\n')
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"1\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_length_pixels.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"2\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_width_pixels.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"3\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_area_pixels.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"4\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_perimeter_pixels.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"5\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_eqd_pixels.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"6\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_area_convexity.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"7\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results +
"/images/plot_area_ratio_of_convexity.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"8\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_aspect_ratio.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"9\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_compactness.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"10\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_number_of_teeth.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"11\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_perimeter_convexity.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"12\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results +
"/images/plot_perimeter_ratio_of_length.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"13\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results +
"/images/plot_perimeter_ratio_of_length_and_width.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"14\" width=\"400\" />"
html_index = my_html_boxplot_pixels.index(string_to_change)
my_html_boxplot_pixels[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_roundness.png")
str_for_html = "\n".join(my_html_boxplot_pixels)
boxplot_pixels.write(str_for_html)
boxplot_pixels.close()
boxplot_template.close()
boxplot_pixels_string = Parameters.results + '/html/html_boxplot_pixels.html'
self.config_file.html_boxplot_pixels_output_config_file(
boxplot_pixels_string)
### CM ####
boxplot_cm = open(Parameters.results + '/html/html_boxplot_cm.html',
'w')
boxplot_template = open(
Parameters.resources + '/html/boxplot_template.html', "r")
my_html_boxplot_cm = boxplot_template.read().split('\n')
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"1\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_length_cm.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"2\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_width_cm.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"3\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_area_cm.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"4\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_perimeter_cm.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"5\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_eqd_cm.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"6\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_area_convexity.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"7\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results +
"/images/plot_area_ratio_of_convexity.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"8\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_aspect_ratio.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"9\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_compactness.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"10\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_number_of_teeth.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"11\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_perimeter_convexity.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"12\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results +
"/images/plot_perimeter_ratio_of_length.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"13\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results +
"/images/plot_perimeter_ratio_of_length_and_width.png")
string_to_change = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"14\" width=\"400\" />"
html_index = my_html_boxplot_cm.index(string_to_change)
my_html_boxplot_cm[
html_index] = "<img style=\"float: left; margin: 0px 0px 15px 15px;\" src=\"%s\" width=\"400\" />" % (
Parameters.results + "/images/plot_roundness.png")
str_for_html = "\n".join(my_html_boxplot_cm)
boxplot_cm.write(str_for_html)
boxplot_cm.close()
boxplot_template.close()
boxplot_cm_string = Parameters.results + '/html/html_boxplot_cm.html'
self.config_file.html_boxplot_cm_output_config_file(boxplot_cm_string)
def __init__(self, path):
self.images = []
self.path = path
self.config_file = ConfigMaker(self.path)
self.image_name = ""
class HtmlMaker:
def __init__(self, path):
self.images = []
self.path = path
self.config_file = ConfigMaker(self.path)
self.image_name = ""
#self.config_file = ConfigMaker(Parameters.results + "/summary_output.config")
def accession_area_pixel_maker(self, rep_area, image_name):
self.image_name = image_name
accession_area_plot_html_file = Parameters.results + "/html/"+ self.image_name+"_accession_area_violin.html"
outF = open(accession_area_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_single_area.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Area]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % rep_area
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + accession_area_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.accession_area_plot_html_output_config_file(accession_area_plot_html_file)
#####################
print "Adding area pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Area of seeds in accession in Pixels")
plt.boxplot(rep_area, 0, 'rs', 0)
boxplot_path_accession_area_pixels = Parameters.results + "/images/"+self.image_name+"_plot_accession_area_pixels.png"
savefig(boxplot_path_accession_area_pixels)
self.config_file.accession_area_pixels_boxplot_output_config_file(boxplot_path_accession_area_pixels)
def accession_eqd_pixel_maker(self, rep_eqd,image_name):
self.image_name = image_name
accession_eqd_plot_html_file = Parameters.results + '/html/'+self.image_name+'_accession_eqd_violin.html'
outF = open(accession_eqd_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_single_eqd.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Eqd]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % rep_eqd
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + accession_eqd_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.accession_eqd_plot_html_output_config_file(accession_eqd_plot_html_file)
#####################
print "Adding equivalent diameter pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Equivalent Diameter of seeds in accession in Pixels")
plt.boxplot(rep_eqd, 0, 'rs', 0)
boxplot_path_accession_eqd_pixels = Parameters.results + "/images/"+self.image_name+"_plot_accession_eqd_pixels.png"
savefig(boxplot_path_accession_eqd_pixels)
self.config_file.accession_eqd_pixels_boxplot_output_config_file(boxplot_path_accession_eqd_pixels)
def accession_perimeter_pixel_maker(self, rep_perimeter, image_name):
self.image_name = image_name
accession_perimeter_plot_html_file = Parameters.results + '/html/'+self.image_name+'_accession_perimeter_violin.html'
outF = open(accession_perimeter_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_single_perimeter.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Perimeter]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % rep_perimeter
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + accession_perimeter_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.accession_perimeter_plot_html_output_config_file(accession_perimeter_plot_html_file)
#####################
print "Adding perimeter pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Perimeter of seeds in accession in Pixels")
plt.boxplot(rep_perimeter, 0, 'rs', 0)
boxplot_path_accession_perimeter_pixels = Parameters.results + "/images/"+self.image_name+"_plot_accession_perimeter_pixels.png"
savefig(boxplot_path_accession_perimeter_pixels)
self.config_file.accession_perimeter_pixels_boxplot_output_config_file(boxplot_path_accession_perimeter_pixels)
def accession_seed_table_file_maker(self,seed_table, image_name):
self.image_name = image_name
accession_seed_table_file = Parameters.results + "/html/"+self.image_name+"_accession_seed_table.html"
outTable = open(accession_seed_table_file, "w")
inTable = open(Parameters.resources + '/html/index.html', "r")
my_html_test_doc = inTable.read().split('\n')
string_to_be_substituted = "THIS IS TABLE"
html_index = my_html_test_doc.index(string_to_be_substituted)
my_html_test_doc[html_index] = seed_table
str_for_html = "\n".join(my_html_test_doc)
outTable.write(str_for_html)
outTable.close()
inTable.close()
filename_plot = 'file://' + accession_seed_table_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.accession_table_html_output_config_file(accession_seed_table_file)
def accession_method_html_maker(self, original_image_jpg_file, hsv_jpg_file,mask_png_file,seed_labels_jpg_file,imposed_annotation_jpg_file, image_name):
self.image_name = image_name
seed_method_file = Parameters.results + "/html/"+self.image_name+"_accession_method_seed.html"
outF = open(seed_method_file, "w")
inF = open(Parameters.resources + '/html/method_index.html', "r")
my_html_test_doc_method = inF.read().split('\n')
string_to_be_substituted = "<img class=\"card-img-top\" data-src=\"PICTURE\" alt=\"Card image cap\">"
html_index = my_html_test_doc_method.index(string_to_be_substituted)
method_string = "<img class=\"card-img-top\" src=\"%s\" alt=\"Card image cap\">" % original_image_jpg_file
my_html_test_doc_method[html_index] = method_string
string_to_be_substituted = "<img class=\"card-img-top\" data-src=\"PICTURE2\" alt=\"Card image cap\">"
html_index = my_html_test_doc_method.index(string_to_be_substituted)
method_string = "<img class=\"card-img-top\" src=\"%s\" alt=\"Card image cap\">" % hsv_jpg_file
my_html_test_doc_method[html_index] = method_string
string_to_be_substituted = "<img class=\"card-img-top\" data-src=\"PICTURE3\" alt=\"Card image cap\">"
html_index = my_html_test_doc_method.index(string_to_be_substituted)
method_string = "<img class=\"card-img-top\" src=\"%s\" alt=\"Card image cap\">" % mask_png_file
my_html_test_doc_method[html_index] = method_string
string_to_be_substituted = "<img class=\"card-img-top\" data-src=\"PICTURE4\" alt=\"Card image cap\">"
html_index = my_html_test_doc_method.index(string_to_be_substituted)
method_string = "<img class=\"card-img-top\" src=\"%s\" alt=\"Card image cap\">" % seed_labels_jpg_file
my_html_test_doc_method[html_index] = method_string
string_to_be_substituted = "<img class=\"card-img-top\" data-src=\"PICTURE5\" alt=\"Card image cap\">"
html_index = my_html_test_doc_method.index(string_to_be_substituted)
method_string = "<img class=\"card-img-top\" src=\"%s\" alt=\"Card image cap\">" % imposed_annotation_jpg_file
my_html_test_doc_method[html_index] = method_string
str_for_html = "\n".join(my_html_test_doc_method)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + seed_method_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.accession_method_html_output_config_file(seed_method_file)
def summary_table_maker(self, summary_csv_file):
print "Making html summary."
summary_file = open(summary_csv_file, "r")
columns = ['Accession',
'Number of Seeds',
'Mean Area Pixels',
'Mean Equivalent Diameter Pixels',
'Mean Perimeter Pixels']
df = pd.read_csv(summary_file, names=columns)
html_table = df.to_html(justify='left')
list_seed_table = html_table.split('\n')
del list_seed_table[0]
del list_seed_table[-1]
seed_table_summary = "\n".join(list_seed_table)
summary_file.close()
summary_seed_html_table_file = Parameters.results + "/html/summary_seed_table.html"
outTable = open(summary_seed_html_table_file, "w")
inTable = open(Parameters.resources + '/html/index.html', "r")
my_html_test_doc = inTable.read().split('\n')
string_to_be_substituted = "THIS IS TABLE"
html_index = my_html_test_doc.index(string_to_be_substituted)
my_html_test_doc[html_index] = seed_table_summary
str_for_html = "\n".join(my_html_test_doc)
outTable.write(str_for_html)
outTable.close()
inTable.close()
filename_plot = 'file://' + summary_seed_html_table_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.summary_table_html_output_config_file(summary_seed_html_table_file)
self.config_file.summary_csv_output_config_file(summary_csv_file)
summary_file.close()
def summary_perimeter_pixel_maker(self):
summaryfile = open(Parameters.results + "/tables/workfile.csv", "r")
header_names = ["Accession",
"Number of Seeds",
"Mean Area Pixels",
"Mean Equivalent Diameter Pixels",
"Mean Perimeter Pixels"]
df = pd.read_csv(summaryfile, names=header_names)
summary_perimeter = []
for i in df["Mean Perimeter Pixels"]:
summary_perimeter.append(i)
summary_perimeter_plot_html_file = Parameters.results + '/html/summary_perimeter_violin.html'
outF = open(summary_perimeter_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_single_perimeter.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Perimeter]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % summary_perimeter
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + summary_perimeter_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.summary_perimter_pixels_html_output_config_file(summary_perimeter_plot_html_file)
#####################
print "Adding summary perimeter pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Average Perimeter of seeds in summary in Pixels")
plt.boxplot(summary_perimeter, 0, 'rs', 0)
boxplot_path_summary_perimeter_pixels = Parameters.results + "/images/plot_summary_perimeter_pixels.png"
savefig(boxplot_path_summary_perimeter_pixels)
self.config_file.summary_perimeter_pixels_boxplot_output_config_file(boxplot_path_summary_perimeter_pixels)
def summary_area_pixel_maker(self):
summaryfile = open(Parameters.results + "/tables/workfile.csv", "r")
header_names = ["image_name",
"numberofseeds",
"area_mean_pix",
"eqd_mean_pix",
"perimeter_mean_pix",
"mean_max_mins",
"pix_per_cm",
"area_mean_cm",
"eqd_mean_cm",
"perimeter_mean_cm"]
df = pd.read_csv(summaryfile, names=header_names)
summary_area = []
for i in df["area_mean_pix"]:
summary_area.append(i)
summary_area_plot_html_file = Parameters.results + '/html/summary_area_violin.html'
outF = open(summary_area_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_single_area.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Area]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % summary_area
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + summary_area_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.summary_area_pixels_html_output_config_file(summary_area_plot_html_file)
#####################
print "Adding summary area pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Average Area of seeds in summary in Pixels")
plt.boxplot(summary_area, 0, 'rs', 0)
boxplot_path_summary_area_pixels = Parameters.results + "/images/plot_summary_area_pixels.png"
savefig(boxplot_path_summary_area_pixels)
self.config_file.summary_area_pixels_boxplot_output_config_file(boxplot_path_summary_area_pixels)
def summary_eqd_pixel_maker(self):
summaryfile = open(Parameters.results + "/tables/workfile.csv", "r")
header_names = ["image_name",
"numberofseeds",
"area_mean_pix",
"eqd_mean_pix",
"perimeter_mean_pix",
"mean_max_mins",
"pix_per_cm",
"area_mean_cm",
"eqd_mean_cm",
"perimeter_mean_cm"]
df = pd.read_csv(summaryfile, names=header_names)
summary_eqd = []
for i in df["eqd_mean_pix"]:
summary_eqd.append(i)
summary_eqd_plot_html_file = Parameters.results + '/html/summary_eqd_violin.html'
outF = open(summary_eqd_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_single_eqd.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Eqd]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % summary_eqd
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + summary_eqd_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.summary_eqd_pixels_html_output_config_file(summary_eqd_plot_html_file)
#####################
print "Adding summary eqd pixels boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Average Equivalent Diameter of seeds in summary in Pixels")
plt.boxplot(summary_eqd, 0, 'rs', 0)
boxplot_path_summary_eqd_pixels = Parameters.results + "/images/plot_summary_eqd_pixels.png"
savefig(boxplot_path_summary_eqd_pixels)
self.config_file.summary_eqd_pixels_boxplot_output_config_file(boxplot_path_summary_eqd_pixels)
def summary_numberofseeds_pixel_maker(self):
summaryfile = open(Parameters.results + "/tables/workfile.csv", "r")
header_names = ["image_name",
"numberofseeds",
"area_mean_pix",
"eqd_mean_pix",
"perimeter_mean_pix",
"mean_max_mins",
"pix_per_cm",
"area_mean_cm",
"eqd_mean_cm",
"perimeter_mean_cm"]
df = pd.read_csv(summaryfile, names=header_names)
summary_number_of_seeds = []
for i in df["numberofseeds"]:
summary_number_of_seeds.append(i)
summary_number_of_seeds_plot_html_file = Parameters.results + '/html/summary_numberofseeds_violin.html'
outF = open(summary_number_of_seeds_plot_html_file, "w")
inF = open(Parameters.resources + '/html/index_summary_numberofseeds.html', "r")
my_html_test_doc_plot = inF.read().split('\n')
string_to_be_substituted = "var x10=[Number]"
html_index = my_html_test_doc_plot.index(string_to_be_substituted)
my_html_test_doc_plot[html_index] = "var x10=%s" % summary_number_of_seeds
str_for_html = "\n".join(my_html_test_doc_plot)
outF.write(str_for_html)
outF.close()
inF.close()
filename_plot = 'file://' + summary_number_of_seeds_plot_html_file
#webbrowser.get().open_new_tab(filename_plot)
self.config_file.summary_numberofseeds_html_output_config_file(summary_number_of_seeds_plot_html_file)
#####################
print "Adding summary number of seeds boxplot to config file."
pos = [1]
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(20, 20))
plt.figure()
plt.xlabel("Number of seeds in summary")
plt.boxplot(summary_number_of_seeds, 0, 'rs', 0)
boxplot_path_summary_number_of_seeds= Parameters.results + "/images/plot_summary_number_of_seeds.png"
savefig(boxplot_path_summary_number_of_seeds)
self.config_file.summary_number_of_seeds_boxplot_output_config_file(boxplot_path_summary_number_of_seeds)