sqed 0.5.8 → 0.7.1
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- checksums.yaml +4 -4
- data/.ruby-version +1 -1
- data/.travis.yml +4 -2
- data/lib/sqed/boundaries.rb +1 -1
- data/lib/sqed/boundary_finder/color_line_finder.rb +124 -39
- data/lib/sqed/boundary_finder.rb +13 -10
- data/lib/sqed/error.rb +2 -0
- data/lib/sqed/extractor.rb +3 -3
- data/lib/sqed/parser.rb +2 -1
- data/lib/sqed/version.rb +1 -1
- data/lib/sqed.rb +11 -6
- data/lib/sqed_config.rb +53 -15
- data/spec/lib/sqed_config_spec.rb +2 -4
- data/spec/lib/sqed_spec.rb +8 -10
- data/spec/lib/stage_handling/horizontal_offset_cross_spec.rb +3 -1
- data/spec/lib/stage_handling/inverted_t_stage_spec.rb +61 -0
- data/spec/lib/stage_handling/lep_stage2_spec.rb +64 -0
- data/spec/lib/stage_handling/seven_slot_spec.rb +91 -16
- data/spec/lib/stage_handling/t_stage_spec.rb +61 -0
- data/spec/spec_helper.rb +1 -1
- data/spec/support/files/stage_images/inhs_7_slot3.jpg +0 -0
- data/spec/support/files/stage_images/inverted_t_stage.png +0 -0
- data/spec/support/files/stage_images/lep_stage2.jpg +0 -0
- data/spec/support/files/stage_images/lep_stage3.jpg +0 -0
- data/spec/support/files/stage_images/t_stage.png +0 -0
- data/spec/support/image_helpers.rb +25 -8
- data/sqed.gemspec +4 -4
- metadata +32 -15
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 0a10699c845a53421c6ea0446eac442be0470448d0c55c876bb849c2ec4a928e
|
4
|
+
data.tar.gz: b15da56bbbd2146e8683c7c19bcf3df8712c9bdb43c4015f173992e111b52520
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 1f7b7798e7e21145b3d46da2f68ff8b5bd83f341a7926d894d3f7253e5551eafa8297a26bd5fb0053707acca91c2fec2db42638bc27b54c13d58986b8ab6a051
|
7
|
+
data.tar.gz: b5ba7f2552f5db764f9436c77b874e7c094369d554a6df44ac15342a40177a7a80531fe1c3d87d2a34b725deeef21adec53fab1a311e0de7bf55e4a3ced64194
|
data/.ruby-version
CHANGED
@@ -1 +1 @@
|
|
1
|
-
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1
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+
3.0.2
|
data/.travis.yml
CHANGED
@@ -3,7 +3,7 @@
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|
3
3
|
language: ruby
|
4
4
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dist: bionic
|
5
5
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rvm:
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6
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-
- 2.
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6
|
+
- 2.7.1
|
7
7
|
#before_install:
|
8
8
|
# - sudo add-apt-repository -y ppa:moti-p/cc
|
9
9
|
# - sudo apt-get update
|
@@ -12,9 +12,11 @@ rvm:
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|
12
12
|
before_install:
|
13
13
|
- sudo apt-get update -qq
|
14
14
|
- sudo apt-get install -qq tesseract-ocr tesseract-ocr-nld
|
15
|
+
- sudo sed -i 's/name="disk" value="1GiB"/name="disk" value="8GiB"/' /etc/ImageMagick-6/policy.xml
|
16
|
+
- identify -list resource | grep Disk | grep 8GiB # Check ImageMagick setting is actually working.
|
15
17
|
branches:
|
16
18
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only:
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17
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-
-
|
19
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+
- main
|
18
20
|
notifications:
|
19
21
|
email:
|
20
22
|
- diapriid@gmail.com
|
data/lib/sqed/boundaries.rb
CHANGED
@@ -24,7 +24,7 @@ class Sqed
|
|
24
24
|
attr_accessor :complete
|
25
25
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|
26
26
|
def initialize(layout = nil)
|
27
|
-
raise 'unrecognized layout' if layout && !SqedConfig::LAYOUTS.include?(layout)
|
27
|
+
raise Sqed::Error, 'unrecognized layout' if layout && !SqedConfig::LAYOUTS.include?(layout)
|
28
28
|
@complete = false
|
29
29
|
|
30
30
|
@layout = layout
|
@@ -15,7 +15,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
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|
15
15
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|
16
16
|
super(image: image, layout: layout, use_thumbnail: use_thumbnail)
|
17
17
|
|
18
|
-
raise 'No layout provided.' if @layout.nil?
|
18
|
+
raise Sqed::Error, 'No layout provided.' if @layout.nil?
|
19
19
|
|
20
20
|
# !@#? why this
|
21
21
|
@boundary_color = boundary_color
|
@@ -29,34 +29,39 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
29
29
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|
30
30
|
private
|
31
31
|
|
32
|
+
# boundaries.coordinates are referenced from stage image
|
33
|
+
#
|
34
|
+
# A reminder that boundaries are x1,y1, width, height
|
32
35
|
def find_bands
|
33
|
-
case layout # boundaries.coordinates are referenced from stage image
|
34
36
|
|
35
|
-
|
37
|
+
# see config/sqed_config.rb
|
38
|
+
case layout
|
39
|
+
|
40
|
+
when :cross # 4 windows, with perfectly intersected horizontal and vertical division
|
36
41
|
v = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
37
|
-
h = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries
|
42
|
+
h = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries
|
38
43
|
|
39
44
|
return if v.nil? || h.nil?
|
40
45
|
|
41
|
-
boundaries.set(0, [0,0, v.width_for(0), h.height_for(0) ])
|
42
|
-
boundaries.set(1, [ v.x_for(1), 0, v.width_for(1), h.height_for(0) ])
|
43
|
-
boundaries.set(2, [ v.x_for(1), h.y_for(1), v.width_for(1), h.height_for(1) ])
|
44
|
-
boundaries.set(3, [0, h.y_for(1), v.width_for(0), h.height_for(1) ])
|
46
|
+
boundaries.set(0, [0,0, v.width_for(0), h.height_for(0) ])
|
47
|
+
boundaries.set(1, [ v.x_for(1), 0, v.width_for(1), h.height_for(0) ])
|
48
|
+
boundaries.set(2, [ v.x_for(1), h.y_for(1), v.width_for(1), h.height_for(1) ])
|
49
|
+
boundaries.set(3, [0, h.y_for(1), v.width_for(0), h.height_for(1) ])
|
45
50
|
|
46
51
|
# No specs for this yet
|
47
52
|
when :horizontal_offset_cross
|
48
53
|
horizontal = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
49
54
|
|
50
|
-
itop = image.crop(*horizontal.for(0), true)
|
55
|
+
itop = image.crop(*horizontal.for(0), true)
|
51
56
|
ibottom = image.crop(*horizontal.for(1), true)
|
52
57
|
|
53
58
|
top = self.class.new(image: itop, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
54
59
|
bottom = self.class.new(image: ibottom, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
55
60
|
|
56
|
-
boundaries.set(0, [0, 0, top.width_for(0), top.height_for(0) ])
|
57
|
-
boundaries.set(1, [top.x_for(1), 0, top.width_for(1), top.height_for(1) ])
|
58
|
-
boundaries.set(2, [bottom.x_for(1), horizontal.y_for(1), bottom.width_for(1), bottom.height_for(1) ])
|
59
|
-
boundaries.set(3, [0, horizontal.y_for(1), bottom.width_for(0), bottom.height_for(0) ])
|
61
|
+
boundaries.set(0, [0, 0, top.width_for(0), top.height_for(0) ])
|
62
|
+
boundaries.set(1, [top.x_for(1), 0, top.width_for(1), top.height_for(1) ])
|
63
|
+
boundaries.set(2, [bottom.x_for(1), horizontal.y_for(1), bottom.width_for(1), bottom.height_for(1) ])
|
64
|
+
boundaries.set(3, [0, horizontal.y_for(1), bottom.width_for(0), bottom.height_for(0) ])
|
60
65
|
|
61
66
|
when :lep_stage
|
62
67
|
top_bottom_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color) # detect vertical division [array]
|
@@ -64,9 +69,9 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
64
69
|
|
65
70
|
boundaries.set(6, [0, top_bottom_split[2], left_right_split[0], image.rows - top_bottom_split[2]] )
|
66
71
|
|
67
|
-
left_top_image = image.crop( 0, 0, left_right_split[0], top_bottom_split[0], true)
|
72
|
+
left_top_image = image.crop( 0, 0, left_right_split[0], top_bottom_split[0], true)
|
68
73
|
|
69
|
-
left_top_split =
|
74
|
+
left_top_split =
|
70
75
|
SqedUtils.corrected_frequency(
|
71
76
|
Sqed::BoundaryFinder.color_boundary_finder(image: left_top_image, boundary_color: boundary_color),
|
72
77
|
max_width: left_top_image.columns,
|
@@ -74,8 +79,8 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
74
79
|
)
|
75
80
|
|
76
81
|
boundaries.set(0, [0, 0, left_top_split[1], top_bottom_split[0]] ) # keep as 1 for safety
|
77
|
-
|
78
|
-
boundaries.set(1, [left_top_split[2], 0, left_top_image.columns - left_top_split[2], top_bottom_split[0]] )
|
82
|
+
|
83
|
+
boundaries.set(1, [left_top_split[2], 0, left_top_image.columns - left_top_split[2], top_bottom_split[0]] )
|
79
84
|
boundaries.set(2, [left_right_split[2], 0, image.columns - left_right_split[0], top_bottom_split[0]] )
|
80
85
|
|
81
86
|
bottom_right_image = image.crop(left_right_split[2], top_bottom_split[2], image.columns - left_right_split[2], image.rows - top_bottom_split[2], true)
|
@@ -89,7 +94,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
89
94
|
|
90
95
|
boundaries.set(3, [left_right_split[2] + bottom_right_split[2], top_bottom_split[2], image.columns - bottom_right_split[2], image.rows - top_bottom_split[2] ] )
|
91
96
|
|
92
|
-
bottom_right_left_image = image.crop(left_right_split[2], top_bottom_split[2], bottom_right_split[0], image.rows - top_bottom_split[2], true)
|
97
|
+
bottom_right_left_image = image.crop(left_right_split[2], top_bottom_split[2], bottom_right_split[0], image.rows - top_bottom_split[2], true)
|
93
98
|
|
94
99
|
bottom_right_left_split =
|
95
100
|
SqedUtils.corrected_frequency(
|
@@ -101,25 +106,104 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
101
106
|
boundaries.set(4, [left_right_split[2], top_bottom_split[2], bottom_right_image.columns - bottom_right_left_image.columns, bottom_right_left_split[0] ] )
|
102
107
|
|
103
108
|
boundaries.set(5, [
|
104
|
-
left_right_split[2],
|
109
|
+
left_right_split[2],
|
105
110
|
top_bottom_split[2] + bottom_right_left_split[2],
|
106
111
|
bottom_right_image.columns - bottom_right_left_image.columns,
|
107
|
-
bottom_right_left_image.rows - bottom_right_left_split[2]
|
112
|
+
bottom_right_left_image.rows - bottom_right_left_split[2]
|
108
113
|
])
|
109
114
|
|
115
|
+
when :lep_stage2
|
116
|
+
top_bottom_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color) # detect vertical division [array]
|
117
|
+
left_right_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, sample_subdivision_size: 2, boundary_color: boundary_color) # detect horizontal division [array]
|
118
|
+
|
119
|
+
boundaries.set(6, [0, top_bottom_split[2], left_right_split[0], image.rows - top_bottom_split[2]] ) # OK
|
120
|
+
|
121
|
+
left_top_image = image.crop( 0, 0, left_right_split[0], top_bottom_split[0], true)
|
122
|
+
|
123
|
+
left_top_split =
|
124
|
+
SqedUtils.corrected_frequency(
|
125
|
+
Sqed::BoundaryFinder.color_boundary_finder(image: left_top_image, boundary_color: boundary_color),
|
126
|
+
max_width: left_top_image.columns,
|
127
|
+
width_factor: 1.8
|
128
|
+
)
|
129
|
+
|
130
|
+
boundaries.set(0, [0, 0, left_top_split[1], top_bottom_split[0]] ) # OK
|
131
|
+
|
132
|
+
boundaries.set(1, [left_top_split[2], 0, left_top_image.columns - left_top_split[2], top_bottom_split[0]] )
|
133
|
+
boundaries.set(2, [left_right_split[2], 0, image.columns - left_right_split[0], top_bottom_split[0]] )
|
134
|
+
|
135
|
+
bottom_right_image = image.crop(left_right_split[2], top_bottom_split[2], image.columns - left_right_split[2], image.rows - top_bottom_split[2], true)
|
136
|
+
|
137
|
+
bottom_right_split =
|
138
|
+
SqedUtils.corrected_frequency(
|
139
|
+
Sqed::BoundaryFinder.color_boundary_finder(image: bottom_right_image, boundary_color: boundary_color, scan: :rows),
|
140
|
+
max_width: bottom_right_image.columns,
|
141
|
+
width_factor: 1.8
|
142
|
+
)
|
143
|
+
|
144
|
+
boundaries.set(3, [
|
145
|
+
left_right_split[2] + bottom_right_split[2],
|
146
|
+
top_bottom_split[2],
|
147
|
+
image.columns - bottom_right_split[2],
|
148
|
+
top_bottom_split[0] ])
|
149
|
+
|
150
|
+
bottom_right_left_image = image.crop(left_right_split[2], top_bottom_split[2], bottom_right_split[0], image.rows - top_bottom_split[2], true)
|
151
|
+
|
152
|
+
bottom_right_left_top_bottom_split =
|
153
|
+
SqedUtils.corrected_frequency(
|
154
|
+
Sqed::BoundaryFinder.color_boundary_finder(image: bottom_right_left_image, scan: :columns, boundary_color: boundary_color),
|
155
|
+
max_width: bottom_right_left_image.columns,
|
156
|
+
width_factor: 1.8
|
157
|
+
)
|
158
|
+
|
159
|
+
boundaries.set(4, [
|
160
|
+
left_right_split[2],
|
161
|
+
top_bottom_split[2] + bottom_right_left_top_bottom_split[2],
|
162
|
+
bottom_right_left_image.columns,
|
163
|
+
bottom_right_left_top_bottom_split[2]
|
164
|
+
])
|
165
|
+
|
166
|
+
|
167
|
+
boundaries.set(5, [
|
168
|
+
left_right_split[2],
|
169
|
+
top_bottom_split[2],
|
170
|
+
bottom_right_left_image.columns,
|
171
|
+
bottom_right_left_top_bottom_split[0],
|
172
|
+
])
|
173
|
+
|
174
|
+
when :t
|
175
|
+
horizontal = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
176
|
+
|
177
|
+
bottom = image.crop(*horizontal.for(1), true)
|
178
|
+
btm_split = self.class.new(image: bottom, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
179
|
+
|
180
|
+
boundaries.set(0, horizontal.for(0))
|
181
|
+
boundaries.set(1, [ btm_split.x_for(1), horizontal.height_for(0), btm_split.width_for(1), btm_split.height_for(1) ] )
|
182
|
+
boundaries.set(2, [ 0, horizontal.height_for(0), btm_split.width_for(0), btm_split.height_for(0) ] )
|
183
|
+
|
184
|
+
when :inverted_t
|
185
|
+
horizontal = self.class.new(image: @image, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
186
|
+
|
187
|
+
top = image.crop(*horizontal.for(0), true)
|
188
|
+
top_split = self.class.new(image: top, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
189
|
+
|
190
|
+
boundaries.set(0, [ 0,0, top_split.width_for(0), top_split.height_for(0)] )
|
191
|
+
boundaries.set(1, [ top_split.width_for(0), 0, top_split.width_for(1), top_split.height_for(1)] )
|
192
|
+
boundaries.set(2, horizontal.for(1))
|
193
|
+
|
110
194
|
when :right_t
|
111
195
|
vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
112
196
|
|
113
197
|
irt = image.crop(*vertical.for(1), true)
|
114
198
|
right = self.class.new(image: irt, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries
|
115
199
|
|
116
|
-
boundaries.set(0, vertical.for(0))
|
117
|
-
boundaries.set(1, [ vertical.x_for(1), 0, right.width_for(0), right.height_for(0) ] )
|
118
|
-
boundaries.set(2, [ vertical.x_for(1), right.y_for(1), right.width_for(1), right.height_for(1)] )
|
200
|
+
boundaries.set(0, vertical.for(0))
|
201
|
+
boundaries.set(1, [ vertical.x_for(1), 0, right.width_for(0), right.height_for(0) ] )
|
202
|
+
boundaries.set(2, [ vertical.x_for(1), right.y_for(1), right.width_for(1), right.height_for(1)] )
|
119
203
|
|
120
204
|
when :seven_slot
|
121
205
|
top_bottom_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, scan: :columns, boundary_color: boundary_color) # detect vertical division [array]
|
122
|
-
left_right_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, sample_subdivision_size:
|
206
|
+
left_right_split = Sqed::BoundaryFinder.color_boundary_finder(image: image, sample_subdivision_size: 1, boundary_color: boundary_color) # detect horizontal division [array]
|
123
207
|
|
124
208
|
boundaries.set(0, [0, 0, left_right_split[0], top_bottom_split[0]])
|
125
209
|
boundaries.set(6, [0, top_bottom_split[2], left_right_split[0], image.rows - top_bottom_split[2]] )
|
@@ -128,18 +212,22 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
128
212
|
right_bottom_image = image.crop(left_right_split[2], top_bottom_split[2], image.columns - left_right_split[2], image.rows - top_bottom_split[2], true) # sections 3,4,5
|
129
213
|
|
130
214
|
right_top_split = ::SqedUtils.corrected_frequency(
|
131
|
-
Sqed::BoundaryFinder.color_boundary_finder(
|
132
|
-
|
133
|
-
|
215
|
+
Sqed::BoundaryFinder.color_boundary_finder(
|
216
|
+
image: right_top_image, boundary_color: boundary_color, scan: :rows),
|
217
|
+
width_factor: 1.8,
|
218
|
+
max_width: right_top_image.columns
|
134
219
|
) # vertical line b/w 1 & 2, use "corrected_frequency" to account for color bleed from previous crop
|
135
220
|
|
136
221
|
boundaries.set(1, [left_right_split[2], 0, right_top_split[0], top_bottom_split[0]] )
|
137
222
|
boundaries.set(2, [left_right_split[2] + right_top_split[2], 0, right_top_image.columns - right_top_split[2], top_bottom_split[0]])
|
138
223
|
|
139
224
|
right_bottom_split = SqedUtils.corrected_frequency(
|
140
|
-
Sqed::BoundaryFinder.color_boundary_finder(
|
141
|
-
|
142
|
-
|
225
|
+
Sqed::BoundaryFinder.color_boundary_finder(
|
226
|
+
image: right_bottom_image,
|
227
|
+
scan: :columns,
|
228
|
+
sample_subdivision_size: 2, boundary_color: boundary_color),
|
229
|
+
width_factor: 1.8,
|
230
|
+
max_width: right_bottom_image.rows) # horizontal line b/w (5,3) & 4, use "corrected_frequency" to account for color bleed from previous crop
|
143
231
|
|
144
232
|
bottom_right_top_image = right_bottom_image.crop(0,0, image.columns - left_right_split[2], right_bottom_split[0], true) # 3,5
|
145
233
|
|
@@ -151,18 +239,18 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
151
239
|
when :vertical_offset_cross # 4 zones expected, with (varying) horizontal division in left- and right- sides of vertical division
|
152
240
|
vertical = self.class.new(image: @image, layout: :vertical_split, boundary_color: boundary_color, use_thumbnail: false).boundaries
|
153
241
|
|
154
|
-
ilt = image.crop(*vertical.for(0), true)
|
242
|
+
ilt = image.crop(*vertical.for(0), true)
|
155
243
|
irt = image.crop(*vertical.for(1), true)
|
156
244
|
|
157
245
|
left = self.class.new(image: ilt, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false).boundaries # fails
|
158
246
|
right = self.class.new(image: irt, layout: :horizontal_split, boundary_color: boundary_color, use_thumbnail: false ).boundaries # OK
|
159
247
|
|
160
|
-
boundaries.set(0, [0, 0, left.width_for(0), left.height_for(0) ])
|
161
|
-
boundaries.set(1, [vertical.x_for(1), 0, right.width_for(0), right.height_for(0) ])
|
162
|
-
boundaries.set(2, [vertical.x_for(1), right.y_for(1), right.width_for(1), right.height_for(1) ])
|
163
|
-
boundaries.set(3, [0, left.y_for(1), left.width_for(1), left.height_for(1) ])
|
248
|
+
boundaries.set(0, [0, 0, left.width_for(0), left.height_for(0) ])
|
249
|
+
boundaries.set(1, [vertical.x_for(1), 0, right.width_for(0), right.height_for(0) ])
|
250
|
+
boundaries.set(2, [vertical.x_for(1), right.y_for(1), right.width_for(1), right.height_for(1) ])
|
251
|
+
boundaries.set(3, [0, left.y_for(1), left.width_for(1), left.height_for(1) ])
|
164
252
|
|
165
|
-
when :vertical_split
|
253
|
+
when :vertical_split
|
166
254
|
t = Sqed::BoundaryFinder.color_boundary_finder(image: image, boundary_color: boundary_color) #detect vertical division
|
167
255
|
return if t.nil?
|
168
256
|
boundaries.set(0, [0, 0, t[0], image.rows]) # left section of image
|
@@ -175,10 +263,7 @@ class Sqed::BoundaryFinder::ColorLineFinder < Sqed::BoundaryFinder
|
|
175
263
|
boundaries.set(0, [0, 0, image.columns, t[0]]) # upper section of image
|
176
264
|
boundaries.set(1, [0, t[2], image.columns, image.rows - t[2]]) # lower section of image
|
177
265
|
|
178
|
-
|
179
|
-
|
180
266
|
else # no @layout provided !?
|
181
|
-
|
182
267
|
boundaries.set(0, [0, 0, image.columns, image.rows]) # totality of image as default
|
183
268
|
end
|
184
269
|
|
data/lib/sqed/boundary_finder.rb
CHANGED
@@ -6,6 +6,7 @@ class Sqed
|
|
6
6
|
#
|
7
7
|
class BoundaryFinder
|
8
8
|
|
9
|
+
# Problemantic (e.g. seven slot) seem to resolve at ~360
|
9
10
|
THUMB_SIZE = 100
|
10
11
|
COLOR_DELTA = 1.3 # color (e.g. red) must be this much be *COLOR_DELTA > than other values (e.g. blue/green)
|
11
12
|
|
@@ -18,7 +19,8 @@ class Sqed
|
|
18
19
|
# A Sqed::Boundaries instance, stores the coordinates of all of the layout sections
|
19
20
|
attr_reader :boundaries
|
20
21
|
|
21
|
-
#
|
22
|
+
# @return Boolean
|
23
|
+
# Whether to compress the original image to a thumbnail when finding boundaries at certain steps of the processing
|
22
24
|
attr_reader :use_thumbnail
|
23
25
|
|
24
26
|
# when we compute using a derived thumbnail we temporarily store the full size image here
|
@@ -31,8 +33,8 @@ class Sqed
|
|
31
33
|
@layout = opts[:layout]
|
32
34
|
@image = opts[:image]
|
33
35
|
|
34
|
-
raise 'No layout provided.' if layout.nil?
|
35
|
-
raise 'No image provided.' if image.nil? || image.class.name != 'Magick::Image'
|
36
|
+
raise Sqed::Error, 'No layout provided.' if layout.nil?
|
37
|
+
raise Sqed::Error, 'No image provided.' if image.nil? || image.class.name != 'Magick::Image'
|
36
38
|
|
37
39
|
true
|
38
40
|
end
|
@@ -135,7 +137,7 @@ class Sqed
|
|
135
137
|
while attempts < 5 do
|
136
138
|
samples_to_take = (image_width / sample_subdivision_size).to_i - 1
|
137
139
|
border_hits = sample_border(image, boundary_color, samples_to_take, sample_subdivision_size, scan)
|
138
|
-
|
140
|
+
|
139
141
|
break if border_hits.select{|k,v| v > 1}.size > 2 || sample_subdivision_size == 1
|
140
142
|
|
141
143
|
sample_subdivision_size = (sample_subdivision_size.to_f / 2.0).to_i
|
@@ -164,7 +166,7 @@ class Sqed
|
|
164
166
|
elsif scan == :columns
|
165
167
|
j = image.crop(s * sample_subdivision_size, 0, 1, image.rows, true)
|
166
168
|
else
|
167
|
-
raise
|
169
|
+
raise Sqed::Error
|
168
170
|
end
|
169
171
|
|
170
172
|
j.each_pixel do |pixel, c, r|
|
@@ -207,7 +209,7 @@ class Sqed
|
|
207
209
|
# the start, mid, endpoint position of all (pixel) positions that have a count greater than the cutoff
|
208
210
|
def self.frequency_stats(frequency_hash, sample_cutoff = 0)
|
209
211
|
|
210
|
-
return nil if sample_cutoff.nil? ||
|
212
|
+
return nil if sample_cutoff.nil? || sample_cutoff < 1
|
211
213
|
hit_ranges = []
|
212
214
|
|
213
215
|
frequency_hash.each do |position, count|
|
@@ -236,6 +238,11 @@ class Sqed
|
|
236
238
|
[hit_ranges.first, hit_ranges[(hit_ranges.length / 2).to_i], hit_ranges.last]
|
237
239
|
end
|
238
240
|
|
241
|
+
def self.max_difference(array)
|
242
|
+
array.max - array.min
|
243
|
+
end
|
244
|
+
|
245
|
+
# Usused
|
239
246
|
|
240
247
|
# Returns an Integer, the maximum of the pairwise differences of the values in the array
|
241
248
|
# For example, given
|
@@ -248,10 +255,6 @@ class Sqed
|
|
248
255
|
(0..array.length - 2).map{|i| (array[i] - array[i + 1]).abs }.max
|
249
256
|
end
|
250
257
|
|
251
|
-
def self.max_difference(array)
|
252
|
-
array.max - array.min
|
253
|
-
end
|
254
|
-
|
255
258
|
def self.derivative_signs(array)
|
256
259
|
(0..array.length - 2).map { |i| (array[i + 1] - array[i]) <=> 0 }
|
257
260
|
end
|
data/lib/sqed/error.rb
ADDED
data/lib/sqed/extractor.rb
CHANGED
@@ -23,9 +23,9 @@ class Sqed
|
|
23
23
|
@boundaries = opts[:boundaries]
|
24
24
|
@image = opts[:image]
|
25
25
|
|
26
|
-
raise Error, 'boundaries not provided or provided boundary is not a Sqed::Boundaries' if boundaries.nil? || !boundaries.class == Sqed::Boundaries
|
27
|
-
raise Error, 'metadata_map not provided or metadata_map not a Hash' if metadata_map.nil? || !metadata_map.class == Hash
|
28
|
-
raise Error, 'image not provided' if image.nil? || !image.class.name == 'Magick::Image'
|
26
|
+
raise Sqed::Error, 'boundaries not provided or provided boundary is not a Sqed::Boundaries' if boundaries.nil? || !boundaries.class.name == 'Sqed::Boundaries'
|
27
|
+
raise Sqed::Error, 'metadata_map not provided or metadata_map not a Hash' if metadata_map.nil? || !metadata_map.class.name == 'Hash'
|
28
|
+
raise Sqed::Error, 'image not provided' if image.nil? || !image.class.name == 'Magick::Image'
|
29
29
|
end
|
30
30
|
|
31
31
|
def result
|
data/lib/sqed/parser.rb
CHANGED
@@ -9,8 +9,9 @@ class Sqed::Parser
|
|
9
9
|
attr_accessor :extracted_text
|
10
10
|
|
11
11
|
def initialize(image)
|
12
|
+
raise Sqed::Error, 'no image passed to parser' if image.nil?
|
13
|
+
raise Sqed::Error, 'image is not a Magick::Image' if !(image.class.name == 'Magick::Image')
|
12
14
|
@image = image
|
13
|
-
raise 'no image provided to parser' if @image && !(@image.class.name == 'Magick::Image')
|
14
15
|
end
|
15
16
|
|
16
17
|
end
|
data/lib/sqed/version.rb
CHANGED
data/lib/sqed.rb
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
# encoding: UTF-8
|
2
2
|
|
3
3
|
recent_ruby = RUBY_VERSION >= '2.4.1'
|
4
|
-
raise 'IMPORTANT: sqed gem requires ruby >= 2.4.1' unless recent_ruby
|
4
|
+
raise Sqed::Error, 'IMPORTANT: sqed gem requires ruby >= 2.4.1' unless recent_ruby
|
5
5
|
|
6
6
|
require 'rmagick'
|
7
7
|
require 'sqed_utils'
|
@@ -17,10 +17,12 @@ require 'sqed_utils'
|
|
17
17
|
#
|
18
18
|
class Sqed
|
19
19
|
|
20
|
+
require_relative 'sqed/error'
|
20
21
|
require_relative 'sqed_config'
|
21
22
|
require_relative 'sqed/extractor'
|
22
23
|
require_relative 'sqed/result'
|
23
24
|
|
25
|
+
|
24
26
|
# initial image which is an instance of ImageMagick::Image, containing background and stage, or just stage
|
25
27
|
attr_accessor :image
|
26
28
|
|
@@ -68,6 +70,7 @@ class Sqed
|
|
68
70
|
# Provide a metadata map, overrides metadata taken from pattern
|
69
71
|
attr_accessor :metadata_map
|
70
72
|
|
73
|
+
# @return [Sqed::BoundaryFinder::<Klass>]
|
71
74
|
# Provide a boundary_finder, overrides metadata taken from pattern
|
72
75
|
attr_accessor :boundary_finder
|
73
76
|
|
@@ -165,6 +168,8 @@ class Sqed
|
|
165
168
|
configure_layout(opts)
|
166
169
|
configure_metadata_map(opts)
|
167
170
|
|
171
|
+
raise Sqed::Error, 'boundary_finder not provided' if @boundary_finder.nil?
|
172
|
+
|
168
173
|
@has_border = opts[:has_border]
|
169
174
|
@has_border = true if @has_border.nil?
|
170
175
|
|
@@ -178,18 +183,18 @@ class Sqed
|
|
178
183
|
def configure_from_pattern(value)
|
179
184
|
return if value.nil?
|
180
185
|
value = value.to_sym
|
181
|
-
raise "provided extraction pattern '#{value}' not defined" if !SqedConfig::EXTRACTION_PATTERNS.keys.include?(value)
|
186
|
+
raise Sqed::Error, "provided extraction pattern '#{value}' not defined" if !SqedConfig::EXTRACTION_PATTERNS.keys.include?(value)
|
182
187
|
@pattern = value
|
183
188
|
a = SqedConfig::EXTRACTION_PATTERNS[pattern]
|
184
189
|
@boundary_finder = a[:boundary_finder]
|
185
190
|
@layout = a[:layout]
|
186
191
|
@metadata_map = a[:metadata_map]
|
192
|
+
|
187
193
|
true
|
188
194
|
end
|
189
195
|
|
190
196
|
def configure_boundary_finder(opts)
|
191
|
-
@boundary_finder = opts[:boundary_finder]
|
192
|
-
@boundary_finder ||= Sqed::BoundaryFinder::CrossFinder
|
197
|
+
@boundary_finder = opts[:boundary_finder] if !opts[:boundary_finder].nil?
|
193
198
|
end
|
194
199
|
|
195
200
|
def configure_layout(opts)
|
@@ -212,7 +217,7 @@ class Sqed
|
|
212
217
|
end
|
213
218
|
|
214
219
|
def get_section_boundaries
|
215
|
-
boundary_finder.new(section_params).boundaries
|
220
|
+
boundary_finder.new(**section_params).boundaries
|
216
221
|
end
|
217
222
|
|
218
223
|
# @return [Hash]
|
@@ -232,7 +237,7 @@ class Sqed
|
|
232
237
|
if boundary.populated?
|
233
238
|
@stage_boundary.set(0, boundary.for(0))
|
234
239
|
else
|
235
|
-
raise 'error detecting stage'
|
240
|
+
raise Sqed::Error, 'error detecting stage'
|
236
241
|
end
|
237
242
|
else
|
238
243
|
@stage_boundary.set(0, [0, 0, image.columns, image.rows])
|
data/lib/sqed_config.rb
CHANGED
@@ -17,33 +17,40 @@ require_relative 'sqed/boundary_finder/color_line_finder'
|
|
17
17
|
module SqedConfig
|
18
18
|
|
19
19
|
# Layouts refer to the arrangement of the divided stage.
|
20
|
-
# Windows are enumerated from the top left, moving around the border
|
20
|
+
# Windows are enumerated from the top left, moving around the border
|
21
21
|
# in a clockwise position. For example:
|
22
22
|
#
|
23
23
|
# 0 | 1
|
24
24
|
# ----|---- :cross (any cross pattern)
|
25
25
|
# |
|
26
26
|
# 3 | 2
|
27
|
-
#
|
27
|
+
#
|
28
28
|
#
|
29
29
|
# 0 | 1
|
30
30
|
# |
|
31
|
-
# --------- :horizontal_offset_cross
|
31
|
+
# --------- :horizontal_offset_cross
|
32
32
|
# 3 | 2
|
33
|
-
#
|
33
|
+
#
|
34
34
|
#
|
35
35
|
# 0
|
36
36
|
# -------- :horizontal_split
|
37
37
|
# 1
|
38
|
-
#
|
38
|
+
#
|
39
39
|
#
|
40
40
|
# 0 | 1 | 2
|
41
41
|
# ------------
|
42
42
|
# | 5 | :lep_stage
|
43
|
-
# 6 |---- 3
|
43
|
+
# 6 |---- 3
|
44
44
|
# | 4 |
|
45
45
|
#
|
46
46
|
#
|
47
|
+
# 0 | 1 | 2
|
48
|
+
# --------------
|
49
|
+
# | 5 | :lep_stage2
|
50
|
+
# 6 |---- 3
|
51
|
+
# | 4 |
|
52
|
+
#
|
53
|
+
#
|
47
54
|
# | 1
|
48
55
|
# 0 |---- :right_t
|
49
56
|
# | 2
|
@@ -55,28 +62,41 @@ module SqedConfig
|
|
55
62
|
# 6 |--------
|
56
63
|
# | 4
|
57
64
|
#
|
58
|
-
#
|
65
|
+
#
|
59
66
|
# 0 | 1
|
60
67
|
# |____
|
61
|
-
# ----| :vertical_offset_cross
|
68
|
+
# ----| :vertical_offset_cross
|
62
69
|
# 3 | 2
|
63
|
-
#
|
64
70
|
#
|
65
|
-
#
|
66
|
-
#
|
67
|
-
#
|
71
|
+
#
|
72
|
+
# |
|
73
|
+
# 0 | 1 :vertical_split
|
74
|
+
# |
|
68
75
|
#
|
69
76
|
# -----
|
70
|
-
# | 0 |
|
77
|
+
# | 0 | :internal_box
|
71
78
|
# -----
|
72
|
-
#
|
79
|
+
#
|
80
|
+
# 0 | 1 :inverted_t
|
81
|
+
# -----
|
82
|
+
# 2
|
83
|
+
#
|
84
|
+
# 0 :t
|
85
|
+
# -----
|
86
|
+
# 2 | 1
|
87
|
+
#
|
88
|
+
#
|
89
|
+
#
|
73
90
|
# Hash values are used to stub out
|
74
91
|
# the Sqed::Boundaries instance.
|
75
92
|
LAYOUTS = {
|
93
|
+
t: [0,1,2],
|
94
|
+
inverted_t: [0, 1, 2],
|
76
95
|
cross: [0, 1, 2, 3],
|
77
96
|
horizontal_offset_cross: [0, 1, 2, 3],
|
78
97
|
horizontal_split: [0, 1],
|
79
98
|
lep_stage: [0, 1, 2, 3, 4, 5, 6],
|
99
|
+
lep_stage2: [0, 1, 2, 3, 4, 5, 6],
|
80
100
|
right_t: [0, 1, 2],
|
81
101
|
seven_slot: [0, 1, 2, 3, 4, 5, 6],
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82
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vertical_offset_cross: [0, 1, 2, 3],
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@@ -93,7 +113,7 @@ module SqedConfig
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93
113
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:identifier, # the section contains an identifier (e.g. barcode or unique number)
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94
114
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:image_registration, # the section contains only image registration information,
|
95
115
|
:labels, # the section contains collecting event and other non-determination labels
|
96
|
-
:nothing, # section is empty
|
116
|
+
:nothing, # section is empty
|
97
117
|
:other_labels, # the section that contains text that misc.
|
98
118
|
:specimen, # the specimen only, no metadata should be present
|
99
119
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:stage, # the image contains the full stage
|
@@ -115,6 +135,18 @@ module SqedConfig
|
|
115
135
|
}.freeze
|
116
136
|
|
117
137
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EXTRACTION_PATTERNS = {
|
138
|
+
t: {
|
139
|
+
boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
|
140
|
+
layout: :t,
|
141
|
+
metadata_map: { 0 => :annotated_specimen, 1 => :identifier, 2 => :image_registration }
|
142
|
+
},
|
143
|
+
|
144
|
+
inverted_t: {
|
145
|
+
boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
|
146
|
+
layout: :inverted_t,
|
147
|
+
metadata_map: { 0 => :identifier, 1 => :image_registration, 2 => :annotated_specimen }
|
148
|
+
},
|
149
|
+
|
118
150
|
cross: {
|
119
151
|
boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
|
120
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|
layout: :cross,
|
@@ -139,6 +171,12 @@ module SqedConfig
|
|
139
171
|
metadata_map: { 0 => :curator_metadata, 1 => :collecting_event_labels, 2 => :image_registration, 3 => :identifier, 4 => :other_labels, 5 => :determination_labels, 6 => :specimen }
|
140
172
|
},
|
141
173
|
|
174
|
+
lep_stage2: {
|
175
|
+
boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
|
176
|
+
layout: :lep_stage2,
|
177
|
+
metadata_map: { 0 => :curator_metadata, 1 => :collecting_event_labels, 2 => :image_registration, 3 => :identifier, 4 => :other_labels, 5 => :determination_labels, 6 => :specimen }
|
178
|
+
},
|
179
|
+
|
142
180
|
right_t: {
|
143
181
|
boundary_finder: Sqed::BoundaryFinder::ColorLineFinder,
|
144
182
|
layout: :right_t,
|
@@ -7,13 +7,11 @@ describe SqedConfig do
|
|
7
7
|
end
|
8
8
|
|
9
9
|
specify 'layouts' do
|
10
|
-
expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
|
10
|
+
expect(SqedConfig.metadata[:layouts].keys).to contain_exactly(:t, :inverted_t, :cross, :horizontal_offset_cross, :horizontal_split, :lep_stage, :lep_stage2, :right_t, :seven_slot, :vertical_offset_cross, :vertical_split)
|
11
11
|
end
|
12
12
|
|
13
13
|
specify 'layouts are in patterns' do
|
14
|
-
expect(SqedConfig.metadata[:layouts].keys + [:stage]).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys)
|
14
|
+
expect(SqedConfig.metadata[:layouts].keys + [:stage]).to contain_exactly(*SqedConfig::EXTRACTION_PATTERNS.keys)
|
15
15
|
end
|
16
16
|
|
17
|
-
|
18
|
-
|
19
17
|
end
|