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Maciej Wielgosz
instance_segmentation_classic
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c0cde8d5
Commit
c0cde8d5
authored
2 years ago
by
Maciej Wielgosz
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first version for the sweep test pipeline
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pipeline_test.py
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c0cde8d5
import
subprocess
import
wandb
# local imports
from
metrics.instance_segmentation_metrics_in_folder
import
InstanceSegmentationMetricsInFolder
# wandb.login()
# wandb.init(project="instance_segmentation_classic", entity="smart_forest")
# define a class to run the command with arguments
class
RunCommand
:
def
__init__
(
self
,
cmd
,
args
):
self
.
cmd
=
cmd
self
.
args
=
args
def
__call__
(
self
):
print
(
"
Running command:
"
+
self
.
cmd
+
"
"
+
"
"
.
join
(
self
.
args
))
subprocess
.
run
([
self
.
cmd
,
*
self
.
args
])
# define the sweep configuration with the parameters to sweep
sweep_configuration
=
{
'
method
'
:
'
random
'
,
'
name
'
:
'
sweep
'
,
'
metric
'
:
{
'
goal
'
:
'
maximize
'
,
'
name
'
:
'
f1_score
'
},
'
parameters
'
:
{
'
N_TILES
'
:
{
'
values
'
:
[
3
]},
'
SLICE_THICKNESS
'
:
{
'
values
'
:
[
0.5
]},
'
FIND_STEMS_HEIGHT
'
:
{
'
values
'
:
[
1.5
]},
'
FIND_STEMS_THICKNESS
'
:
{
'
values
'
:
[
0.5
]},
'
GRAPH_MAXIMUM_CUMULATIVE_GAP
'
:
{
'
values
'
:
[
3
]},
'
ADD_LEAVES_VOXEL_LENGTH
'
:
{
'
values
'
:
[
0.5
]},
'
FIND_STEMS_MIN_POINTS
'
:
{
'
values
'
:
[
50
,
100
,
150
]}
}
}
def
main
():
# initialize the sweep
run
=
wandb
.
init
(
project
=
"
sweep-train
"
,
entity
=
"
maciej-wielgosz-nibio
"
)
# get files for the sweep
print
(
"
Getting files for the sweep
"
)
cmd
=
"
/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/bash_helper_scripts/get_small_data_for_playground.sh
"
subprocess
.
run
([
cmd
],
shell
=
True
)
# define the arguments for all the parameters from the sweep configuration
print
(
"
Defining arguments for all the parameters from the sweep configuration
"
)
n_tiles
=
wandb
.
config
.
N_TILES
slice_thickness
=
wandb
.
config
.
SLICE_THICKNESS
find_stems_height
=
wandb
.
config
.
FIND_STEMS_HEIGHT
find_stems_thickness
=
wandb
.
config
.
FIND_STEMS_THICKNESS
graph_maximum_cumulative_gap
=
wandb
.
config
.
GRAPH_MAXIMUM_CUMULATIVE_GAP
add_leaves_voxel_length
=
wandb
.
config
.
ADD_LEAVES_VOXEL_LENGTH
find_stems_min_points
=
wandb
.
config
.
FIND_STEMS_MIN_POINTS
# print the arguments
print
(
"
N_TILES:
"
+
str
(
n_tiles
))
print
(
"
SLICE_THICKNESS:
"
+
str
(
slice_thickness
))
print
(
"
FIND_STEMS_HEIGHT:
"
+
str
(
find_stems_height
))
print
(
"
FIND_STEMS_THICKNESS:
"
+
str
(
find_stems_thickness
))
print
(
"
GRAPH_MAXIMUM_CUMULATIVE_GAP:
"
+
str
(
graph_maximum_cumulative_gap
))
print
(
"
ADD_LEAVES_VOXEL_LENGTH:
"
+
str
(
add_leaves_voxel_length
))
print
(
"
FIND_STEMS_MIN_POINTS:
"
+
str
(
find_stems_min_points
))
# define the command
cmd
=
"
./run_all_command_line.sh
"
# define the arguments
args
=
[
"
-d
"
,
"
/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground
"
]
print
(
"
Adding the arguments to the list of arguments
"
)
args
.
extend
([
"
-n
"
,
str
(
n_tiles
),
"
-s
"
,
str
(
slice_thickness
),
"
-h
"
,
str
(
find_stems_height
),
"
-t
"
,
str
(
find_stems_thickness
),
"
-g
"
,
str
(
graph_maximum_cumulative_gap
),
"
-l
"
,
str
(
add_leaves_voxel_length
),
"
-m
"
,
str
(
find_stems_min_points
)
])
# run the command with the arguments
print
(
"
Running the command with the arguments
"
)
RunCommand
(
cmd
,
args
)()
# compute the metric
print
(
"
Computing the metric
"
)
metric
=
InstanceSegmentationMetricsInFolder
(
gt_las_folder_path
=
'
/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/input_data
'
,
target_las_folder_path
=
'
/home/nibio/mutable-outside-world/code/gitlab_fsct/instance_segmentation_classic/sample_playground/results/instance_segmented_point_clouds_with_ground
'
,
gt_label_name
=
'
treeID
'
,
target_label_name
=
'
treeID
'
,
verbose
=
True
)
f1_score
=
metric
.
main
()
print
(
"
F1 score:
"
+
str
(
f1_score
))
# log the metric
print
(
"
Logging the metric
"
)
wandb
.
log
({
"
f1_score
"
:
f1_score
})
# define the sweep
sweep_id
=
wandb
.
sweep
(
sweep
=
sweep_configuration
,
project
=
"
sweep-train
"
,
entity
=
"
maciej-wielgosz-nibio
"
)
# run the sweep
wandb
.
agent
(
sweep_id
,
function
=
main
,
count
=
2
)
\ No newline at end of file
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