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aknecht2
Image Harvest
Commits
43cbafc8
Commit
43cbafc8
authored
Nov 10, 2015
by
aknecht2
Browse files
Increased wall time request for extract-multi script. Added output for alexmac experiment.
parent
01269a68
Changes
9
Expand all
Hide whitespace changes
Inline
Side-by-side
examples/workflows/alexmac/imgproc.json
View file @
43cbafc8
...
...
@@ -24,7 +24,7 @@
"depends"
:
[
"gray"
]
},
{
"name"
:
"thresh"
,
"name"
:
"thresh
old
"
,
"executable"
:
"ih-threshold"
,
"inputs"
:
[
"blurred"
],
"outputs"
:
[
"masked"
],
...
...
@@ -41,7 +41,7 @@
"inputs"
:
[
"masked"
,
"base"
],
"outputs"
:
[
"recolor"
],
"arguments"
:
{},
"depends"
:
[
"thresh"
]
"depends"
:
[
"thresh
old
"
]
},
{
"name"
:
"crop"
,
...
...
@@ -107,7 +107,7 @@
"depends"
:
[
"crop"
]
},
{
"name"
:
"bgr
_
lab"
,
"name"
:
"bgr
2
lab"
,
"executable"
:
"ih-convert-color"
,
"inputs"
:
[
"cf1"
],
"outputs"
:
[
"lab_spectrum"
],
...
...
@@ -125,7 +125,7 @@
"arguments"
:
{
"--logic"
:
"((r - g) > 5)"
},
"depends"
:
[
"bgr
_
lab"
]
"depends"
:
[
"bgr
2
lab"
]
},
{
"name"
:
"labfilter2"
,
...
...
@@ -159,7 +159,7 @@
"inputs"
:
[
"recolor"
],
"outputs"
:
[
"cf2"
],
"arguments"
:
{
"--logic"
:
"(((r - g) < ((i
*
i) / 4000)) or (((r - g) > (40
*
(1 - (i / 765)))) and ((r - b) > (60
*
(1 - (i / 765))))))"
"--logic"
:
"(((r - g) < ((i
.
i) / 4000)) or (((r - g) > (40
.
(1 - (i / 765)))) and ((r - b) > (60
.
(1 - (i / 765))))))"
},
"depends"
:
[
"reconstitute"
]
},
...
...
@@ -301,7 +301,7 @@
]
},
"options"
:
{
"save-steps"
:
"true"
},
"extract"
:
{
"histogram-bin"
:
{
...
...
examples/workflows/alexmac/output/fluo_hist_bins.json
0 → 100644
View file @
43cbafc8
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\ No newline at end of file
examples/workflows/alexmac/output/images.csv
0 → 100644
View file @
43cbafc8
This diff is collapsed.
Click to expand it.
examples/workflows/alexmac/output/img3.db
0 → 100644
View file @
43cbafc8
File added
examples/workflows/alexmac/output/imgproc.log
0 → 100644
View file @
43cbafc8
Image processing error log
==========================
Image with id 'fluosv191' loaded from input path '/home/aknecht/stash/9-22-15_lemnatec_images/alexmac/81715 alexmac_81715-004D_2015-08-17_03-07-09_1855600/Fluo_SV_0_2/0_0_0.png' was not processed successfully.
examples/workflows/alexmac/output/output.db
0 → 100644
View file @
43cbafc8
File added
examples/workflows/alexmac/output/rgb_hist_bins.json
0 → 100644
View file @
43cbafc8
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,
139
,
75
]},
{
"max"
:
[
86
,
255
,
137
],
"name"
:
"rgb_bin74"
,
"min"
:
[
52
,
139
,
100
]},
{
"max"
:
[
86
,
255
,
255
],
"name"
:
"rgb_bin75"
,
"min"
:
[
52
,
139
,
137
]},
{
"max"
:
[
131
,
63
,
57
],
"name"
:
"rgb_bin76"
,
"min"
:
[
86
,
1
,
1
]},
{
"max"
:
[
131
,
63
,
75
],
"name"
:
"rgb_bin77"
,
"min"
:
[
86
,
1
,
57
]},
{
"max"
:
[
131
,
63
,
100
],
"name"
:
"rgb_bin78"
,
"min"
:
[
86
,
1
,
75
]},
{
"max"
:
[
131
,
63
,
137
],
"name"
:
"rgb_bin79"
,
"min"
:
[
86
,
1
,
100
]},
{
"max"
:
[
131
,
63
,
255
],
"name"
:
"rgb_bin80"
,
"min"
:
[
86
,
1
,
137
]},
{
"max"
:
[
131
,
78
,
57
],
"name"
:
"rgb_bin81"
,
"min"
:
[
86
,
63
,
1
]},
{
"max"
:
[
131
,
78
,
75
],
"name"
:
"rgb_bin82"
,
"min"
:
[
86
,
63
,
57
]},
{
"max"
:
[
131
,
78
,
100
],
"name"
:
"rgb_bin83"
,
"min"
:
[
86
,
63
,
75
]},
{
"max"
:
[
131
,
78
,
137
],
"name"
:
"rgb_bin84"
,
"min"
:
[
86
,
63
,
100
]},
{
"max"
:
[
131
,
78
,
255
],
"name"
:
"rgb_bin85"
,
"min"
:
[
86
,
63
,
137
]},
{
"max"
:
[
131
,
102
,
57
],
"name"
:
"rgb_bin86"
,
"min"
:
[
86
,
78
,
1
]},
{
"max"
:
[
131
,
102
,
75
],
"name"
:
"rgb_bin87"
,
"min"
:
[
86
,
78
,
57
]},
{
"max"
:
[
131
,
102
,
100
],
"name"
:
"rgb_bin88"
,
"min"
:
[
86
,
78
,
75
]},
{
"max"
:
[
131
,
102
,
137
],
"name"
:
"rgb_bin89"
,
"min"
:
[
86
,
78
,
100
]},
{
"max"
:
[
131
,
102
,
255
],
"name"
:
"rgb_bin90"
,
"min"
:
[
86
,
78
,
137
]},
{
"max"
:
[
131
,
139
,
57
],
"name"
:
"rgb_bin91"
,
"min"
:
[
86
,
102
,
1
]},
{
"max"
:
[
131
,
139
,
75
],
"name"
:
"rgb_bin92"
,
"min"
:
[
86
,
102
,
57
]},
{
"max"
:
[
131
,
139
,
100
],
"name"
:
"rgb_bin93"
,
"min"
:
[
86
,
102
,
75
]},
{
"max"
:
[
131
,
139
,
137
],
"name"
:
"rgb_bin94"
,
"min"
:
[
86
,
102
,
100
]},
{
"max"
:
[
131
,
139
,
255
],
"name"
:
"rgb_bin95"
,
"min"
:
[
86
,
102
,
137
]},
{
"max"
:
[
131
,
255
,
57
],
"name"
:
"rgb_bin96"
,
"min"
:
[
86
,
139
,
1
]},
{
"max"
:
[
131
,
255
,
75
],
"name"
:
"rgb_bin97"
,
"min"
:
[
86
,
139
,
57
]},
{
"max"
:
[
131
,
255
,
100
],
"name"
:
"rgb_bin98"
,
"min"
:
[
86
,
139
,
75
]},
{
"max"
:
[
131
,
255
,
137
],
"name"
:
"rgb_bin99"
,
"min"
:
[
86
,
139
,
100
]},
{
"max"
:
[
131
,
255
,
255
],
"name"
:
"rgb_bin100"
,
"min"
:
[
86
,
139
,
137
]},
{
"max"
:
[
255
,
63
,
57
],
"name"
:
"rgb_bin101"
,
"min"
:
[
131
,
1
,
1
]},
{
"max"
:
[
255
,
63
,
75
],
"name"
:
"rgb_bin102"
,
"min"
:
[
131
,
1
,
57
]},
{
"max"
:
[
255
,
63
,
100
],
"name"
:
"rgb_bin103"
,
"min"
:
[
131
,
1
,
75
]},
{
"max"
:
[
255
,
63
,
137
],
"name"
:
"rgb_bin104"
,
"min"
:
[
131
,
1
,
100
]},
{
"max"
:
[
255
,
63
,
255
],
"name"
:
"rgb_bin105"
,
"min"
:
[
131
,
1
,
137
]},
{
"max"
:
[
255
,
78
,
57
],
"name"
:
"rgb_bin106"
,
"min"
:
[
131
,
63
,
1
]},
{
"max"
:
[
255
,
78
,
75
],
"name"
:
"rgb_bin107"
,
"min"
:
[
131
,
63
,
57
]},
{
"max"
:
[
255
,
78
,
100
],
"name"
:
"rgb_bin108"
,
"min"
:
[
131
,
63
,
75
]},
{
"max"
:
[
255
,
78
,
137
],
"name"
:
"rgb_bin109"
,
"min"
:
[
131
,
63
,
100
]},
{
"max"
:
[
255
,
78
,
255
],
"name"
:
"rgb_bin110"
,
"min"
:
[
131
,
63
,
137
]},
{
"max"
:
[
255
,
102
,
57
],
"name"
:
"rgb_bin111"
,
"min"
:
[
131
,
78
,
1
]},
{
"max"
:
[
255
,
102
,
75
],
"name"
:
"rgb_bin112"
,
"min"
:
[
131
,
78
,
57
]},
{
"max"
:
[
255
,
102
,
100
],
"name"
:
"rgb_bin113"
,
"min"
:
[
131
,
78
,
75
]},
{
"max"
:
[
255
,
102
,
137
],
"name"
:
"rgb_bin114"
,
"min"
:
[
131
,
78
,
100
]},
{
"max"
:
[
255
,
102
,
255
],
"name"
:
"rgb_bin115"
,
"min"
:
[
131
,
78
,
137
]},
{
"max"
:
[
255
,
139
,
57
],
"name"
:
"rgb_bin116"
,
"min"
:
[
131
,
102
,
1
]},
{
"max"
:
[
255
,
139
,
75
],
"name"
:
"rgb_bin117"
,
"min"
:
[
131
,
102
,
57
]},
{
"max"
:
[
255
,
139
,
100
],
"name"
:
"rgb_bin118"
,
"min"
:
[
131
,
102
,
75
]},
{
"max"
:
[
255
,
139
,
137
],
"name"
:
"rgb_bin119"
,
"min"
:
[
131
,
102
,
100
]},
{
"max"
:
[
255
,
139
,
255
],
"name"
:
"rgb_bin120"
,
"min"
:
[
131
,
102
,
137
]},
{
"max"
:
[
255
,
255
,
57
],
"name"
:
"rgb_bin121"
,
"min"
:
[
131
,
139
,
1
]},
{
"max"
:
[
255
,
255
,
75
],
"name"
:
"rgb_bin122"
,
"min"
:
[
131
,
139
,
57
]},
{
"max"
:
[
255
,
255
,
100
],
"name"
:
"rgb_bin123"
,
"min"
:
[
131
,
139
,
75
]},
{
"max"
:
[
255
,
255
,
137
],
"name"
:
"rgb_bin124"
,
"min"
:
[
131
,
139
,
100
]},
{
"max"
:
[
255
,
255
,
255
],
"name"
:
"rgb_bin125"
,
"min"
:
[
131
,
139
,
137
]}]
\ No newline at end of file
examples/workflows/alexmac/stats.json
0 → 100644
View file @
43cbafc8
{
"rgb"
:
[
{
"name"
:
"area"
,
"executable"
:
"pcv-stats-shoot-area"
,
"inputs"
:
[
"images"
],
"outputs"
:
[
"shootarea"
],
"arguments"
:
{
"--group"
:
{
"rgb"
:
[
"rgbsv"
]
}
},
"depends"
:
[
"bin"
]
},
{
"name"
:
"normal"
,
"executable"
:
"pcv-stats-normalize"
,
"inputs"
:
[
"shootarea"
],
"outputs"
:
[
"normal"
],
"arguments"
:
{
"--column"
:
"pixels"
},
"depends"
:
[
"area"
]
},
{
"name"
:
"threshold"
,
"executable"
:
"pcv-stats-threshold"
,
"inputs"
:
[
"normal"
],
"outputs"
:
[
"thresh"
],
"arguments"
:
{
"--thresh"
:
0.01
},
"depends"
:
[
"normal"
]
}
]
}
ih/workflow.py
View file @
43cbafc8
...
...
@@ -383,16 +383,17 @@ class Statistics(Workflow):
Creates the pegasus submit script. submit.sh
"""
with
open
(
self
.
basepath
+
"/"
+
loc
+
"/submit.sh"
,
"w"
)
as
wh
:
submit
=
textwrap
.
dedent
(
"""
\
#!/bin/bash
%s
plan=`pegasus-plan
\\
--conf "%s"
\\
--sites "%s"
\\
--dir "%s"
\\
--output-site local
\\
--dax "%s"
\\
--randomdir
\\
"""
%
(
self
.
basepath
+
"/"
+
loc
+
"/conf.rc"
,
"condorpool"
if
"osg"
in
self
.
config
else
"local"
,
self
.
basepath
+
"/work/stats"
,
self
.
basepath
+
"/"
+
loc
+
"/stats.dax"
))
--randomdir
\\
"""
%
(
"module unload python/2.7"
if
"osg"
in
self
.
config
else
""
,
self
.
basepath
+
"/"
+
loc
+
"/conf.rc"
,
"condorpool"
if
"osg"
in
self
.
config
else
"local"
,
self
.
basepath
+
"/work/stats"
,
self
.
basepath
+
"/"
+
loc
+
"/stats.dax"
))
if
"cluster"
in
self
.
config
:
submit
+=
"""--cluster horizontal
\\\n
"""
submit
+=
textwrap
.
dedent
(
"""
\
...
...
@@ -693,8 +694,8 @@ class ImageProcessor(Workflow):
arguments
[
"--createdb"
]
=
""
arguments
[
"--inputs"
]
=
" "
.
join
([
x
for
x
in
exInput
[
type
][
q
].
keys
()
if
".png"
in
x
])
self
.
_addFile
(
type
+
str
(
q
)
+
".db"
,
type
,
"output"
)
self
.
_addJob
(
type
+
"_extract"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{
"db"
:
{
"file"
:
type
+
str
(
q
)
+
".db"
,
"transfer"
:
False
}},
arguments
,
exDep
[
type
][
q
],
walltime
=
24
0
)
self
.
_addJob
(
type
+
"_extract"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{
"db"
:
{
"file"
:
type
+
str
(
q
)
+
".db"
,
"transfer"
:
False
}},
arguments
,
[],
dax
=
self
.
exdax
,
walltime
=
24
0
)
self
.
_addJob
(
type
+
"_extract"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{
"db"
:
{
"file"
:
type
+
str
(
q
)
+
".db"
,
"transfer"
:
False
}},
arguments
,
exDep
[
type
][
q
],
walltime
=
30
0
)
self
.
_addJob
(
type
+
"_extract"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{
"db"
:
{
"file"
:
type
+
str
(
q
)
+
".db"
,
"transfer"
:
False
}},
arguments
,
[],
dax
=
self
.
exdax
,
walltime
=
30
0
)
maprc
.
write
(
type
+
str
(
q
)
+
".db"
+
" file://"
+
self
.
basepath
+
"/output/"
+
type
+
str
(
q
)
+
".db"
+
" pool=
\"
local
\"\n
"
)
binDep
.
append
(
type
+
"_extract"
+
str
(
q
))
aggIn
[
type
+
str
(
q
)
+
".db"
]
=
{
"file"
:
type
+
str
(
q
)
+
".db"
,
"transfer"
:
False
}
...
...
@@ -726,8 +727,8 @@ class ImageProcessor(Workflow):
exInput
[
type
][
q
][
"db"
]
=
{
"file"
:
type
+
str
(
q
)
+
".db"
,
"transfer"
:
False
}
exInput
[
type
][
q
][
"binfile"
]
=
{
"file"
:
map
[
type
]
+
"_hist_bins.json"
,
"transfer"
:
False
}
arguments
[
"--bins"
]
=
"binfile"
self
.
_addJob
(
type
+
"_extractBins"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{},
arguments
,
[
"bin_creation"
],
walltime
=
2
40
)
self
.
_addJob
(
type
+
"_extractBins"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{},
arguments
,
[
"bin_creation"
],
dax
=
self
.
exdax
,
walltime
=
2
40
)
self
.
_addJob
(
type
+
"_extractBins"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{},
arguments
,
[
"bin_creation"
],
walltime
=
4
8
0
)
self
.
_addJob
(
type
+
"_extractBins"
+
str
(
q
),
"ih-extract-multi"
,
exInput
[
type
][
q
],
{},
arguments
,
[
"bin_creation"
],
dax
=
self
.
exdax
,
walltime
=
4
8
0
)
binDep
.
append
(
type
+
"_extractBins"
+
str
(
q
))
aggIn
[
"db"
]
=
{
"file"
:
"img2.db"
,
"transfer"
:
False
}
self
.
_addJob
(
"sql_aggregate2"
,
"ih-sql-aggregate"
,
aggIn
,
{
"img3.db"
:
{
"file"
:
"img3.db"
,
"transfer"
:
True
}},
{
"--db"
:
"db"
,
"--output"
:
"img3.db"
,
"--inputs"
:
" "
.
join
([
aggIn
[
x
][
"file"
]
for
x
in
aggIn
if
x
!=
"db"
])},
binDep
)
...
...
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