spotifier.sort_nicely() - Code Metrics - Inspection of "Update plotting and add rna_plot_dendogram.py" - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — master ( bc1242...f803eb )

by Marcin

created 2021-04-16 11:25 UTC

spotifier.sort_nicely() A

↳ Parent: spotifier

Complexity

Conditions

Size

Total Lines	8
Code Lines	5

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	2
eloc	5
nop	1
dl	0
loc	8
rs	10
c	0
b	0
f	0

#!/usr/bin/env python
"""
install to work on psd files: psd-tools3
"""
import argparse
from PIL import Image, ImageChops, Image, ImageDraw, ImageFont, ImageStat
import logging
import os
import re

def trim(im):

    """
    https://stackoverflow.com/questions/10615901/trim-whitespace-using-pil
    """
    bg = Image.new(im.mode, im.size, im.getpixel((1,1)))
    diff = ImageChops.difference(im, bg)
    diff = ImageChops.add(diff, diff, 0.5, -100)  # 1.0
    bbox = diff.getbbox()
    if bbox:
        return im.crop(bbox)
    else: return im

def get_parser():

    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    #parser.add_argument('-', "--", help="", default="")

    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    parser.add_argument("-d", "--debug",
                        action="store_true", help="be even more verbose")

    parser.add_argument("--dont-align",
                        action="store_true", help="don't align dots")
    parser.add_argument("-x", default=165, type=int)
    parser.add_argument("-y", default=120, type=int)
    parser.add_argument("--trim-rms", default=50, type=int)
    parser.add_argument("--size", default=100, type=int)
    parser.add_argument("-a", "--dont-annotate", action="store_true")
    parser.add_argument("map", help='map')
    parser.add_argument("file", help="pre-processed image(s)", nargs='+')
    return parser


def get_rms(im):
    stat = ImageStat.Stat(im)
    #r,g,b = stat.mean
    ## print('bg sum', stat.sum[0])
    ## print('bg mean', stat.mean[0])
    ## print('bg rms', stat.rms[0])
    return stat.rms[0]


def sort_nicely(l):
    """ Sort the given list in the way that humans expect.
    http://blog.codinghorror.com/sorting-for-humans-natural-sort-order/
    """
    def convert(text): return int(text) if text.isdigit() else text
    def alphanum_key(key): return [convert(c) for c in re.split('([0-9]+)', key)]
    l.sort(key=alphanum_key)
    return l


if __name__ == '__main__':
    parser = get_parser()
    args = parser.parse_args()

    if list != type(args.file):
        args.file = [args.file]

    args.file = sort_nicely(args.file)
    
    outputs = []

    for file in args.file:
        logging.basicConfig(
            level=logging.INFO,
            format="%(asctime)s %(message)s",
            handlers=[
                logging.FileHandler("spotifier.log"),
                logging.StreamHandler()
            ])
        logging.info('file: %s ' % (str(args)))

        args.trim = not args.dont_align
        if file.endswith('.psd'):
             try:
                 from psd_tools import PSDImage
             except:
                 print('pip install psd-tools3')

             psd = PSDImage.load(file)
             if 1 or args.verbose:
                 for l in psd.layers:
                     if l.name != 'Background':
                         i = l.as_PIL()
                         #i.save('tmp.png')
                     print(l)
             img = psd.as_PIL()
            ## from PIL import Image, ImageSequence
            ## im = Image.open(args.file)
            ## layers = [frame.copy() for frame in ImageSequence.Iterator(im)]
            ## print(layers)
            ## img = layers
        else:
            img = Image.open(file)

        # load map, into figure
        list_txt = '['
        names = []
        for l in open(args.map):
            if l.strip():
                name = ''
                if '#' in l:
                    l, name = l.split('#')
                names.append(name.strip())  # collect names
                list_txt += '[' + l + '],'
        list_txt += ']'
        figure = eval(list_txt)
        if args.verbose: print('Figure:', figure)

        # format of the plate
        PLATE_FORMAT = [
            [0, 0, 1, 1, 1, 1, 0, 0],
            [0, 1, 1, 1, 1, 1, 1, 0],
            [1, 1, 1, 1, 1, 1, 1, 1],
            [1, 1, 1, 1, 1, 1, 1, 1],
            [1, 1, 1, 1, 1, 1, 1, 1],
            [1, 1, 1, 1, 1, 1, 1, 1],
            [1, 1, 1, 1, 1, 1, 1, 1],
            [0, 1, 1, 1, 1, 1, 1, 0],
            [0, 0, 1, 1, 1, 1, 1, 0],
            ]

        # parameters
        size = args.size
        half = size / 2

        x0 = args.x
        y0 = args.y

        dx = size
        dy = size

        pix = []

        # de novo make pix
        i = 0
        for yi in range(1, 10):  # rows
            y = y0 + dy * (yi - 1)

            f, to = 0, 8
            if yi in [1]:
                f, to = 2, 6
            if yi in [2, 8]:
                f, to = 1, 7
            if yi in [9]:
                f, to = 2, 7

            for xi in range(f, to):
                x = x0 + xi * (dx - 1)
                pix.append([x, y])
                i += 1
                # print(i, yi, f, to, x, y)
            
        x_id = 0
        y_id = 0

        spots = []
        spot_id = 1
        for row in PLATE_FORMAT:
            for i in row:
                #x = x0 + (xshift * x_id)  # 150 * 3
                #y = y0 + (yshift * y_id) # 120 * 3
                #print(x, y)
                if i: #  and y_id == 1:
                    # print('index', spot_id - 1)
                    x, y = pix[spot_id - 1] # index for list
                    #x = x + x0
                    #y = y + y0
                    area = (x - half, y - half, x + half, y + half)
                    cropped_img = img.crop(area)
                    rms = get_rms(img)
                    if args.trim and rms > args.trim_rms:
                        cropped_img = trim(cropped_img)
                    if args.debug:
                        cropped_img.save('auto-' + str(y_id) + '-' + str(x_id) + '.png')
                    if args.verbose: print(spot_id, '----------------',)
                    spot_id += 1
                    spots.append(cropped_img)
                x_id += 1
            y_id += 1 # move row down
            x_id = 0

        extra = 0
        if args.dont_annotate:
            extra = 600
        fig = Image.new('RGB', (len(figure[0]) * 100 + extra, len(figure) * 100))
        draw = ImageDraw.Draw(fig)
        x = 0
        y = 0

        # LOAD FONT
        # font = ImageFont.truetype('Pillow/Tests/fonts/FreeMono.ttf', 40)
        # should work for OSX
        try:
            fnt = 'Helvetica.ttc'
            font = ImageFont.truetype(fnt, size=40)
        except OSError:
            font = ImageFont.load_default() # should work for everything else
        font_bar = ImageFont.truetype(fnt, size=100)
        #####################################################

        picked_wt = False

        # based on the collected spots
        # no build the figure
        for i, row in enumerate(figure):
            spots_text = ''
            row_fig = Image.new('RGB', (len(figure[0]) * 100, len(figure) * 100)) # for calculations, for each raw new one
            row_fig_y = 0
            for s in row:  # spot in row
                # for center something like this https://stackoverflow.com/questions/1970807/center-middle-align-text-with-pil
                # this is for spot or gray box
                if s == 0: # put a gray box here
                    img_box = Image.new('RGB', (100, 100))
                    draw_box = ImageDraw.Draw(img_box)
                    draw_box.rectangle((0,0,100,100), fill ="#808080") # , outline ="red")
                    fig.paste(img_box, (x, y)) # s - 1 # index from 0
                    row_fig.paste(img_box, (x, row_fig_y))
                else:
                    fig.paste(spots[s - 1], (x, y)) # s - 1 # index from 0
                    row_fig.paste(spots[s - 1], (x, row_fig_y))

                # this is extra | 
                # if s == -1:  # put a gray box here
                #    img_box = Image.new('RGB', (100, 100))
                #    draw_box = ImageDraw.Draw(img_box)
                #    # 5 is width of the bar ;-)
                #    draw_box.rectangle((0,0,5,100), fill ="#fff") # , outline ="red")
                #    fig.paste(img_box, (x, y)) # s - 1 # index from 0
                #    row_fig.paste(img_box, (x, row_fig_y))
                #    x -= 100
                    
                spots_text += ' ' + str(s)
                x += 100
            # run it for the whole row
            if not picked_wt:
                wt = get_rms(row_fig)
                picked_wt = True
            row_fig_rms = get_rms(row_fig)
            d = round(row_fig_rms - wt, 1)

            if args.verbose: print("%.2f %.2f ∆" % (round(wt, 2), row_fig_rms), d)
            #print(round(1, 2), )
            # str(x) + '-' + str(y)
            if args.dont_annotate:
                draw.text((x, y), '|', font=font_bar, fill = 'darkgray')
                txt = str(d) + ' #' + str(i + 1) + ' ' +  names[i] + ' ' + spots_text
                draw.text((x + 20, y + 10), txt, font = font, fill ="white", align="center")#, , align ="right")
            y += 100
            x = 0

        fig.show()

        map_name = os.path.splitext(os.path.basename(args.map))[0]
        outfn = os.path.splitext(file)[0] + '_spots_' + map_name + '.png'
        fig.save(outfn)
        outputs.append(outfn)

    if len(outputs) > 1:
        # append files to make the final figure
        width = Image.open(outputs[0]).width
        img = Image.new('RGB', (width, 100 * len(outputs)))
        x = 0
        y = 0
        for output in outputs:
            out_img = Image.open(output)            
            img.paste(out_img, (x, y))              
            y += 100
        draw = ImageDraw.Draw(img)
        draw.line([(0, 0), (3, 3)], fill='orange', width=10)

        map_path = os.path.splitext(args.map)[0]
        img.save(map_path + '_all.png')
        img.show()


1		#!/usr/bin/env python
2		"""
3		install to work on psd files: psd-tools3
4		"""
5		import argparse
6		from PIL import Image, ImageChops, Image, ImageDraw, ImageFont, ImageStat
7		import logging
8		import os
9		import re
10
11	View Code Duplication	def trim(im):
		0 ignored issues – show Duplication introduced 2020-09-12 15:03 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
12		"""
13		https://stackoverflow.com/questions/10615901/trim-whitespace-using-pil
14		"""
15		bg = Image.new(im.mode, im.size, im.getpixel((1,1)))
16		diff = ImageChops.difference(im, bg)
17		diff = ImageChops.add(diff, diff, 0.5, -100) # 1.0
18		bbox = diff.getbbox()
19		if bbox:
20		return im.crop(bbox)
21		else: return im
22
23	View Code Duplication	def get_parser():
		0 ignored issues – show Duplication introduced 2020-06-29 19:56 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
24		parser = argparse.ArgumentParser(
25		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
26
27		#parser.add_argument('-', "--", help="", default="")
28
29		parser.add_argument("-v", "--verbose",
30		action="store_true", help="be verbose")
31		parser.add_argument("-d", "--debug",
32		action="store_true", help="be even more verbose")
33
34		parser.add_argument("--dont-align",
35		action="store_true", help="don't align dots")
36		parser.add_argument("-x", default=165, type=int)
37		parser.add_argument("-y", default=120, type=int)
38		parser.add_argument("--trim-rms", default=50, type=int)
39		parser.add_argument("--size", default=100, type=int)
40		parser.add_argument("-a", "--dont-annotate", action="store_true")
41		parser.add_argument("map", help='map')
42		parser.add_argument("file", help="pre-processed image(s)", nargs='+')
43		return parser
44
45
46		def get_rms(im):
47		stat = ImageStat.Stat(im)
48		#r,g,b = stat.mean
49		## print('bg sum', stat.sum[0])
50		## print('bg mean', stat.mean[0])
51		## print('bg rms', stat.rms[0])
52		return stat.rms[0]
53
54
55		def sort_nicely(l):
56		""" Sort the given list in the way that humans expect.
57		http://blog.codinghorror.com/sorting-for-humans-natural-sort-order/
58		"""
59		def convert(text): return int(text) if text.isdigit() else text
60		def alphanum_key(key): return [convert(c) for c in re.split('([0-9]+)', key)]
61		l.sort(key=alphanum_key)
62		return l
63
64
65		if __name__ == '__main__':
66		parser = get_parser()
67		args = parser.parse_args()
68
69		if list != type(args.file):
70		args.file = [args.file]
71
72		args.file = sort_nicely(args.file)
73
74		outputs = []
75
76		for file in args.file:
77		logging.basicConfig(
78		level=logging.INFO,
79		format="%(asctime)s %(message)s",
80		handlers=[
81		logging.FileHandler("spotifier.log"),
82		logging.StreamHandler()
83		])
84		logging.info('file: %s ' % (str(args)))
85
86		args.trim = not args.dont_align
87		if file.endswith('.psd'):
88		try:
89		from psd_tools import PSDImage
90		except:
91		print('pip install psd-tools3')
92
93		psd = PSDImage.load(file)
94		if 1 or args.verbose:
95		for l in psd.layers:
96		if l.name != 'Background':
97		i = l.as_PIL()
98		#i.save('tmp.png')
99		print(l)
100		img = psd.as_PIL()
101		## from PIL import Image, ImageSequence
102		## im = Image.open(args.file)
103		## layers = [frame.copy() for frame in ImageSequence.Iterator(im)]
104		## print(layers)
105		## img = layers
106		else:
107		img = Image.open(file)
108
109		# load map, into figure
110		list_txt = '['
111		names = []
112		for l in open(args.map):
113		if l.strip():
114		name = ''
115		if '#' in l:
116		l, name = l.split('#')
117		names.append(name.strip()) # collect names
118		list_txt += '[' + l + '],'
119		list_txt += ']'
120		figure = eval(list_txt)
121		if args.verbose: print('Figure:', figure)
122
123		# format of the plate
124		PLATE_FORMAT = [
125		[0, 0, 1, 1, 1, 1, 0, 0],
126		[0, 1, 1, 1, 1, 1, 1, 0],
127		[1, 1, 1, 1, 1, 1, 1, 1],
128		[1, 1, 1, 1, 1, 1, 1, 1],
129		[1, 1, 1, 1, 1, 1, 1, 1],
130		[1, 1, 1, 1, 1, 1, 1, 1],
131		[1, 1, 1, 1, 1, 1, 1, 1],
132		[0, 1, 1, 1, 1, 1, 1, 0],
133		[0, 0, 1, 1, 1, 1, 1, 0],
134		]
135
136		# parameters
137		size = args.size
138		half = size / 2
139
140		x0 = args.x
141		y0 = args.y
142
143		dx = size
144		dy = size
145
146		pix = []
147
148		# de novo make pix
149		i = 0
150		for yi in range(1, 10): # rows
151		y = y0 + dy * (yi - 1)
152
153		f, to = 0, 8
154		if yi in [1]:
155		f, to = 2, 6
156		if yi in [2, 8]:
157		f, to = 1, 7
158		if yi in [9]:
159		f, to = 2, 7
160
161		for xi in range(f, to):
162		x = x0 + xi * (dx - 1)
163		pix.append([x, y])
164		i += 1
165		# print(i, yi, f, to, x, y)
166
167		x_id = 0
168		y_id = 0
169
170		spots = []
171		spot_id = 1
172		for row in PLATE_FORMAT:
173		for i in row:
174		#x = x0 + (xshift * x_id) # 150 * 3
175		#y = y0 + (yshift * y_id) # 120 * 3
176		#print(x, y)
177		if i: # and y_id == 1:
178		# print('index', spot_id - 1)
179		x, y = pix[spot_id - 1] # index for list
180		#x = x + x0
181		#y = y + y0
182		area = (x - half, y - half, x + half, y + half)
183		cropped_img = img.crop(area)
184		rms = get_rms(img)
185		if args.trim and rms > args.trim_rms:
186		cropped_img = trim(cropped_img)
187		if args.debug:
188		cropped_img.save('auto-' + str(y_id) + '-' + str(x_id) + '.png')
189		if args.verbose: print(spot_id, '----------------',)
190		spot_id += 1
191		spots.append(cropped_img)
192		x_id += 1
193		y_id += 1 # move row down
194		x_id = 0
195
196		extra = 0
197		if args.dont_annotate:
198		extra = 600
199		fig = Image.new('RGB', (len(figure[0]) * 100 + extra, len(figure) * 100))
200		draw = ImageDraw.Draw(fig)
201		x = 0
202		y = 0
203
204		# LOAD FONT
205		# font = ImageFont.truetype('Pillow/Tests/fonts/FreeMono.ttf', 40)
206		# should work for OSX
207		try:
208		fnt = 'Helvetica.ttc'
209		font = ImageFont.truetype(fnt, size=40)
210		except OSError:
211		font = ImageFont.load_default() # should work for everything else
212		font_bar = ImageFont.truetype(fnt, size=100)
213		#####################################################
214
215		picked_wt = False
216
217		# based on the collected spots
218		# no build the figure
219		for i, row in enumerate(figure):
220		spots_text = ''
221		row_fig = Image.new('RGB', (len(figure[0]) * 100, len(figure) * 100)) # for calculations, for each raw new one
222		row_fig_y = 0
223		for s in row: # spot in row
224		# for center something like this https://stackoverflow.com/questions/1970807/center-middle-align-text-with-pil
225		# this is for spot or gray box
226		if s == 0: # put a gray box here
227		img_box = Image.new('RGB', (100, 100))
228		draw_box = ImageDraw.Draw(img_box)
229		draw_box.rectangle((0,0,100,100), fill ="#808080") # , outline ="red")
230		fig.paste(img_box, (x, y)) # s - 1 # index from 0
231		row_fig.paste(img_box, (x, row_fig_y))
232		else:
233		fig.paste(spots[s - 1], (x, y)) # s - 1 # index from 0
234		row_fig.paste(spots[s - 1], (x, row_fig_y))
235
236		# this is extra \|
237		# if s == -1: # put a gray box here
238		# img_box = Image.new('RGB', (100, 100))
239		# draw_box = ImageDraw.Draw(img_box)
240		# # 5 is width of the bar ;-)
241		# draw_box.rectangle((0,0,5,100), fill ="#fff") # , outline ="red")
242		# fig.paste(img_box, (x, y)) # s - 1 # index from 0
243		# row_fig.paste(img_box, (x, row_fig_y))
244		# x -= 100
245
246		spots_text += ' ' + str(s)
247		x += 100
248		# run it for the whole row
249		if not picked_wt:
250		wt = get_rms(row_fig)
251		picked_wt = True
252		row_fig_rms = get_rms(row_fig)
253		d = round(row_fig_rms - wt, 1)
		0 ignored issues – show introduced 2020-06-29 19:56 UTC by Report Bug Copy Issue Report The variable `wt` does not seem to be defined for all execution paths. Loading history...
254		if args.verbose: print("%.2f %.2f ∆" % (round(wt, 2), row_fig_rms), d)
255		#print(round(1, 2), )
256		# str(x) + '-' + str(y)
257		if args.dont_annotate:
258		draw.text((x, y), '\|', font=font_bar, fill = 'darkgray')
259		txt = str(d) + ' #' + str(i + 1) + ' ' + names[i] + ' ' + spots_text
260		draw.text((x + 20, y + 10), txt, font = font, fill ="white", align="center")#, , align ="right")
261		y += 100
262		x = 0
263
264		fig.show()
265
266		map_name = os.path.splitext(os.path.basename(args.map))[0]
267		outfn = os.path.splitext(file)[0] + '_spots_' + map_name + '.png'
268		fig.save(outfn)
269		outputs.append(outfn)
270
271		if len(outputs) > 1:
272		# append files to make the final figure
273		width = Image.open(outputs[0]).width
274		img = Image.new('RGB', (width, 100 * len(outputs)))
275		x = 0
276		y = 0
277		for output in outputs:
278		out_img = Image.open(output)
279		img.paste(out_img, (x, y))
280		y += 100
281		draw = ImageDraw.Draw(img)
282		draw.line([(0, 0), (3, 3)], fill='orange', width=10)
283
284		map_path = os.path.splitext(args.map)[0]
285		img.save(map_path + '_all.png')
286		img.show()
287

mmagnus / rna-tools

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spotifier.sort_nicely() A

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