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Nyx
MaggotUBA-adapter
Commits
fcefbbac
Commit
fcefbbac
authored
1 year ago
by
François LAURENT
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Merge branch 'hdf5labels' into 'dev'
Text labels See merge request
!9
parents
5d46423e
5a30d4da
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3 merge requests
!11
Set of commits to be tagged v0.18
,
!10
Set of commits to be tagged v0.17
,
!9
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pyproject.toml
+1
-1
1 addition, 1 deletion
pyproject.toml
src/maggotuba/models/trainers.py
+23
-4
23 additions, 4 deletions
src/maggotuba/models/trainers.py
with
24 additions
and
5 deletions
pyproject.toml
+
1
−
1
View file @
fcefbbac
...
@@ -14,7 +14,7 @@ maggotuba-core = {git = "https://gitlab.pasteur.fr/nyx/MaggotUBA-core", tag = "v
...
@@ -14,7 +14,7 @@ maggotuba-core = {git = "https://gitlab.pasteur.fr/nyx/MaggotUBA-core", tag = "v
torch
=
"^1.11.0"
torch
=
"^1.11.0"
numpy
=
"^1.19.3"
numpy
=
"^1.19.3"
protobuf
=
"3.9.2"
protobuf
=
"3.9.2"
taggingbackends
=
{
git
=
"https://gitlab.pasteur.fr/nyx/TaggingBackends"
,
tag
=
"v0.1
5.3
"
}
taggingbackends
=
{
git
=
"https://gitlab.pasteur.fr/nyx/TaggingBackends"
,
tag
=
"v0.1
6
"
}
[build-system]
[build-system]
requires
=
["poetry-core>
=
1.0
.
0
"]
requires
=
["poetry-core>
=
1.0
.
0
"]
...
...
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src/maggotuba/models/trainers.py
+
23
−
4
View file @
fcefbbac
...
@@ -8,6 +8,7 @@ from taggingbackends.explorer import BackendExplorer, check_permissions
...
@@ -8,6 +8,7 @@ from taggingbackends.explorer import BackendExplorer, check_permissions
import
logging
import
logging
import
json
import
json
import
re
import
re
import
os.path
"""
"""
This model borrows the pre-trained MaggotUBA encoder, substitute a dense layer
This model borrows the pre-trained MaggotUBA encoder, substitute a dense layer
...
@@ -139,7 +140,9 @@ class MaggotTrainer:
...
@@ -139,7 +140,9 @@ class MaggotTrainer:
y
=
self
.
model
(
x
.
to
(
self
.
device
))
y
=
self
.
model
(
x
.
to
(
self
.
device
))
return
y
.
cpu
().
numpy
()
return
y
.
cpu
().
numpy
()
def
prepare_dataset
(
self
,
dataset
):
def
prepare_dataset
(
self
,
dataset
,
training
=
False
):
if
training
:
self
.
model
.
clf
.
config
[
'
training_dataset
'
]
=
str
(
dataset
.
path
)
try
:
try
:
dataset
.
batch_size
dataset
.
batch_size
except
AttributeError
:
except
AttributeError
:
...
@@ -203,7 +206,7 @@ class MaggotTrainer:
...
@@ -203,7 +206,7 @@ class MaggotTrainer:
optimizer
.
step
()
optimizer
.
step
()
def
train
(
self
,
dataset
):
def
train
(
self
,
dataset
):
self
.
prepare_dataset
(
dataset
)
self
.
prepare_dataset
(
dataset
,
training
=
True
)
criterion
=
self
.
init_model_for_training
(
dataset
)
criterion
=
self
.
init_model_for_training
(
dataset
)
# pre-train the classifier with static encoder weights
# pre-train the classifier with static encoder weights
if
self
.
_pretrain_classifier
():
if
self
.
_pretrain_classifier
():
...
@@ -248,10 +251,26 @@ class MaggotTrainer:
...
@@ -248,10 +251,26 @@ class MaggotTrainer:
assert
pred
.
size
==
exp
.
size
assert
pred
.
size
==
exp
.
size
predicted
.
append
(
pred
)
predicted
.
append
(
pred
)
expected
.
append
(
exp
)
expected
.
append
(
exp
)
return
np
.
concatenate
(
predicted
),
np
.
concatenate
(
expected
)
predicted
=
np
.
concatenate
(
predicted
)
expected
=
np
.
concatenate
(
expected
)
predicted
=
[
self
.
labels
[
label
]
for
label
in
predicted
]
expected
=
[
dataset
.
labels
[
label
]
for
label
in
expected
]
return
predicted
,
expected
def
save
(
self
):
def
save
(
self
,
copy_dataset
=
True
):
self
.
model
.
save
()
self
.
model
.
save
()
if
copy_dataset
:
# copy the compiled training dataset into the model directory
try
:
dataset
=
self
.
model
.
clf
.
config
[
'
training_dataset
'
]
except
KeyError
:
pass
else
:
copy
=
self
.
model
.
clf
.
path
/
os
.
path
.
basename
(
dataset
)
with
open
(
copy
,
'
wb
'
)
as
g
:
with
open
(
dataset
,
'
rb
'
)
as
f
:
g
.
write
(
f
.
read
())
check_permissions
(
copy
)
@property
@property
def
root_dir
(
self
):
def
root_dir
(
self
):
...
...
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