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Merged
chantelleleveille merged 18 commits into from
Nov 26, 2024
Merged

Background MIPs for TFE #39

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bc46b7a
write mips for colorizer
chantelleleveille Nov 16, 2024
70666d7
add to colorizer workflow
chantelleleveille Nov 16, 2024
e468b6c
update save pngs
chantelleleveille Nov 18, 2024
780b99e
add backdrops
chantelleleveille Nov 18, 2024
e65f197
rename
chantelleleveille Nov 18, 2024
26cb555
remove old import
chantelleleveille Nov 18, 2024
317e5eb
fix directories
chantelleleveille Nov 19, 2024
fa96758
only add mips in one location
chantelleleveille Nov 19, 2024
7f989a1
allow descriptions be undefined in the glossary dictionary during ite…
chantelleleveille Nov 20, 2024
ff2590b
update doc
chantelleleveille Nov 20, 2024
31392d9
update generate mips function
chantelleleveille Nov 21, 2024
959c921
Update nuc_morph_analysis/lib/visualization/write_data_for_colorizer.py
chantelleleveille Nov 22, 2024
dc3b116
Update nuc_morph_analysis/lib/visualization/write_mips_for_colorizer.py
chantelleleveille Nov 22, 2024
2e13705
PR comments!
chantelleleveille Nov 22, 2024
d0de9b3
update method to explicately show order
chantelleleveille Nov 22, 2024
4675c89
Merge remote-tracking branch 'origin/dev' into TFE_mip
chantelleleveille Nov 22, 2024
c721b38
remove trailing white spaces
chantelleleveille Nov 22, 2024
2dc2f9a
format black
chantelleleveille Nov 22, 2024
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235 changes: 154 additions & 81 deletions nuc_morph_analysis/lib/visualization/write_data_for_colorizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,16 @@
from nuc_morph_analysis.lib.preprocessing.global_dataset_filtering import (
load_dataset_with_features,
)
from nuc_morph_analysis.lib.visualization.write_mips_for_colorizer import (
save_colony_backdrop_mips,
)

from nuc_morph_analysis.lib.visualization.plotting_tools import (
get_plot_labels_for_metric,
)
from nuc_morph_analysis.lib.visualization.glossary import (
GLOSSARY,
)
)

from colorizer_data.writer import ColorizerDatasetWriter
from colorizer_data.writer import (
Expand Down Expand Up @@ -68,13 +72,6 @@ class NucMorphFeatureSpec:
# volume float In FMS manifest Volume of a single nucleus in pixels in a given frame
# height float In FMS manifest Height (in the z-direction) of the a single nucleus in pixels in a given frame
# NUC_PC1 float Needs calculated and added Value for shape mode 1 for a single nucleus in a given frame
# NUC_PC2 float Needs calculated and added Value for shape mode 2 for a single nucleus in a given frame
# NUC_PC3 float Needs calculated and added Value for shape mode 3 for a single nucleus in a given frame
# NUC_PC4 float Needs calculated and added Value for shape mode 4 for a single nucleus in a given frame
# NUC_PC5 float Needs calculated and added Value for shape mode 5 for a single nucleus in a given frame
# NUC_PC6 float Needs calculated and added Value for shape mode 6 for a single nucleus in a given frame
# NUC_PC7 float Needs calculated and added Value for shape mode 7 for a single nucleus in a given frame
# NUC_PC8 float Needs calculated and added Value for shape mode 8 for a single nucleus in a given frame


OBJECT_ID_COLUMN = "label_img"
Expand Down Expand Up @@ -103,7 +100,9 @@ class NucMorphFeatureSpec:
NucMorphFeatureSpec("density"),
NucMorphFeatureSpec("normalized_colony_depth"),
NucMorphFeatureSpec(
"termination", FeatureType.CATEGORICAL, ["Division", "Leaves FOV", "Apoptosis"]
"termination",
FeatureType.CATEGORICAL,
["Division", "Leaves FOV", "Apoptosis"],
),
NucMorphFeatureSpec("distance_from_centroid"),
NucMorphFeatureSpec("neighbor_avg_dxdt_48_volume_whole_colony"),
Expand All @@ -130,7 +129,9 @@ class NucMorphFeatureSpec:
NucMorphFeatureSpec("colony_time_at_B"),
NucMorphFeatureSpec("normalized_colony_depth"),
NucMorphFeatureSpec(
"termination", FeatureType.CATEGORICAL, ["Division", "Leaves FOV", "Apoptosis"]
"termination",
FeatureType.CATEGORICAL,
["Division", "Leaves FOV", "Apoptosis"],
),
NucMorphFeatureSpec("volume_at_A"),
NucMorphFeatureSpec("time_at_A"),
Expand Down Expand Up @@ -165,7 +166,9 @@ class NucMorphFeatureSpec:
NucMorphFeatureSpec("colony_time_at_B"),
NucMorphFeatureSpec("normalized_colony_depth"),
NucMorphFeatureSpec(
"termination", FeatureType.CATEGORICAL, ["Division", "Leaves FOV", "Apoptosis"]
"termination",
FeatureType.CATEGORICAL,
["Division", "Leaves FOV", "Apoptosis"],
),
NucMorphFeatureSpec("volume_at_A"),
NucMorphFeatureSpec("time_at_A"),
Expand Down Expand Up @@ -200,13 +203,19 @@ class NucMorphFeatureSpec:
NucMorphFeatureSpec("colony_time_at_B"),
NucMorphFeatureSpec("normalized_colony_depth"),
NucMorphFeatureSpec(
"termination", FeatureType.CATEGORICAL, ["Division", "Leaves FOV", "Apoptosis"]
"termination",
FeatureType.CATEGORICAL,
["Division", "Leaves FOV", "Apoptosis"],
),
NucMorphFeatureSpec(
"is_growth_outlier", FeatureType.CATEGORICAL, ["False", "True"]
),
NucMorphFeatureSpec("is_growth_outlier", FeatureType.CATEGORICAL, ["False", "True"]),
NucMorphFeatureSpec(
"baseline_colonies_dataset", FeatureType.CATEGORICAL, ["False", "True"]
),
NucMorphFeatureSpec("full_interphase_dataset", FeatureType.CATEGORICAL, ["False", "True"]),
NucMorphFeatureSpec(
"full_interphase_dataset", FeatureType.CATEGORICAL, ["False", "True"]
),
NucMorphFeatureSpec(
"lineage_annotated_dataset", FeatureType.CATEGORICAL, ["False", "True"]
),
Expand All @@ -229,74 +238,109 @@ class NucMorphFeatureSpec:
NucMorphFeatureSpec("SA_fold_change_fromB"),
NucMorphFeatureSpec("delta_SA_BC"),
NucMorphFeatureSpec("SA_vol_ratio"),

# mitotic and apoptotic neighbor columns
NucMorphFeatureSpec(column_name="frame_of_breakdown", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="frame_of_formation", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="number_of_frame_of_breakdown_neighbors"),
NucMorphFeatureSpec(column_name="number_of_frame_of_formation_neighbors"),
NucMorphFeatureSpec(column_name="has_mitotic_neighbor_breakdown", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_mitotic_neighbor_formation", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_mitotic_neighbor_breakdown_forward_dilated", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_mitotic_neighbor_formation_backward_dilated", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_mitotic_neighbor", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_mitotic_neighbor_dilated", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="frame_of_death", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_dying_neighbor", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="has_dying_neighbor_forward_dilated", type=FeatureType.CATEGORICAL, categories=["False", "True"]),
NucMorphFeatureSpec(column_name="number_of_frame_of_death_neighbors"),
NucMorphFeatureSpec(column_name="sum_has_mitotic_neighbor_breakdown"), # per track feature
NucMorphFeatureSpec(column_name="sum_has_mitotic_neighbor_formation"),# per track feature
NucMorphFeatureSpec(column_name="sum_has_mitotic_neighbor"),# per track feature
NucMorphFeatureSpec(column_name="sum_has_dying_neighbor"),# per track feature
NucMorphFeatureSpec(column_name="sum_number_of_frame_of_breakdown_neighbors"),# per track feature
NucMorphFeatureSpec(column_name="number_of_frame_of_death_neighbors"),# per track feature


NucMorphFeatureSpec(
"frame_of_breakdown",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"frame_of_formation",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec("number_of_frame_of_breakdown_neighbors"),
NucMorphFeatureSpec("number_of_frame_of_formation_neighbors"),
NucMorphFeatureSpec(
"has_mitotic_neighbor_breakdown",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"has_mitotic_neighbor_formation",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"has_mitotic_neighbor_breakdown_forward_dilated",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"has_mitotic_neighbor_formation_backward_dilated",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"has_mitotic_neighbor",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"has_mitotic_neighbor_dilated",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"frame_of_death", type=FeatureType.CATEGORICAL, categories=["False", "True"]
),
NucMorphFeatureSpec(
"has_dying_neighbor",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec(
"has_dying_neighbor_forward_dilated",
type=FeatureType.CATEGORICAL,
categories=["False", "True"],
),
NucMorphFeatureSpec("number_of_frame_of_death_neighbors"),
NucMorphFeatureSpec("sum_has_mitotic_neighbor_breakdown"), # per track feature
NucMorphFeatureSpec("sum_has_mitotic_neighbor_formation"), # per track feature
NucMorphFeatureSpec("sum_has_mitotic_neighbor"), # per track feature
NucMorphFeatureSpec("sum_has_dying_neighbor"), # per track feature
NucMorphFeatureSpec(
"sum_number_of_frame_of_breakdown_neighbors"
), # per track feature
NucMorphFeatureSpec("number_of_frame_of_death_neighbors"), # per track feature
# new columns
# useful and likely to make it to final dataset
NucMorphFeatureSpec('2d_area_nuc_cell_ratio'),
NucMorphFeatureSpec('2d_area_nucleus'),
NucMorphFeatureSpec('2d_area_pseudo_cell'),
NucMorphFeatureSpec('2d_area_cyto'),
NucMorphFeatureSpec('2d_intensity_min_edge'),
NucMorphFeatureSpec('2d_intensity_max_edge'),
NucMorphFeatureSpec('2d_intensity_mean_edge'),

NucMorphFeatureSpec("2d_area_nuc_cell_ratio"),
NucMorphFeatureSpec("2d_area_nucleus"),
NucMorphFeatureSpec("2d_area_pseudo_cell"),
NucMorphFeatureSpec("2d_area_cyto"),
NucMorphFeatureSpec("2d_intensity_min_edge"),
NucMorphFeatureSpec("2d_intensity_max_edge"),
NucMorphFeatureSpec("2d_intensity_mean_edge"),
# potentially useful, but likely not needed in final dataset
NucMorphFeatureSpec('2d_convex_area_nucleus'),
NucMorphFeatureSpec('2d_eccentricity_nucleus'),
NucMorphFeatureSpec('2d_equivalent_diameter_nucleus'),
NucMorphFeatureSpec('2d_extent_nucleus'),
NucMorphFeatureSpec('2d_filled_area_nucleus'),
NucMorphFeatureSpec('2d_major_axis_length_nucleus'),
NucMorphFeatureSpec('2d_minor_axis_length_nucleus'),
NucMorphFeatureSpec('2d_orientation_nucleus'),
NucMorphFeatureSpec('2d_perimeter_nucleus'),
NucMorphFeatureSpec('2d_solidity_nucleus'),

NucMorphFeatureSpec("2d_convex_area_nucleus"),
NucMorphFeatureSpec("2d_eccentricity_nucleus"),
NucMorphFeatureSpec("2d_equivalent_diameter_nucleus"),
NucMorphFeatureSpec("2d_extent_nucleus"),
NucMorphFeatureSpec("2d_filled_area_nucleus"),
NucMorphFeatureSpec("2d_major_axis_length_nucleus"),
NucMorphFeatureSpec("2d_minor_axis_length_nucleus"),
NucMorphFeatureSpec("2d_orientation_nucleus"),
NucMorphFeatureSpec("2d_perimeter_nucleus"),
NucMorphFeatureSpec("2d_solidity_nucleus"),
# potentially useful, but likely not needed in final dataset
NucMorphFeatureSpec('2d_convex_area_pseudo_cell'),
NucMorphFeatureSpec('2d_eccentricity_pseudo_cell'),
NucMorphFeatureSpec('2d_equivalent_diameter_pseudo_cell'),
NucMorphFeatureSpec('2d_extent_pseudo_cell'),
NucMorphFeatureSpec('2d_filled_area_pseudo_cell'),
NucMorphFeatureSpec('2d_major_axis_length_pseudo_cell'),
NucMorphFeatureSpec('2d_minor_axis_length_pseudo_cell'),
NucMorphFeatureSpec('2d_orientation_pseudo_cell'),
NucMorphFeatureSpec('2d_perimeter_pseudo_cell'),
NucMorphFeatureSpec('2d_solidity_pseudo_cell'),

NucMorphFeatureSpec("2d_convex_area_pseudo_cell"),
NucMorphFeatureSpec("2d_eccentricity_pseudo_cell"),
NucMorphFeatureSpec("2d_equivalent_diameter_pseudo_cell"),
NucMorphFeatureSpec("2d_extent_pseudo_cell"),
NucMorphFeatureSpec("2d_filled_area_pseudo_cell"),
NucMorphFeatureSpec("2d_major_axis_length_pseudo_cell"),
NucMorphFeatureSpec("2d_minor_axis_length_pseudo_cell"),
NucMorphFeatureSpec("2d_orientation_pseudo_cell"),
NucMorphFeatureSpec("2d_perimeter_pseudo_cell"),
NucMorphFeatureSpec("2d_solidity_pseudo_cell"),
# extra
NucMorphFeatureSpec('inv_cyto_density'),
NucMorphFeatureSpec('2d_perimeter_nuc_cell_ratio'),
NucMorphFeatureSpec('2d_eccentricity_nuc_cell_ratio'),
NucMorphFeatureSpec('label_pseudo_cell'),


NucMorphFeatureSpec("inv_cyto_density"),
NucMorphFeatureSpec("2d_perimeter_nuc_cell_ratio"),
NucMorphFeatureSpec("2d_eccentricity_nuc_cell_ratio"),
NucMorphFeatureSpec("label_pseudo_cell"),
# extra old columns
NucMorphFeatureSpec('colony_depth', type=FeatureType.DISCRETE),

NucMorphFeatureSpec("colony_depth", type=FeatureType.DISCRETE),
],
}

Expand Down Expand Up @@ -336,7 +380,9 @@ def make_frame(
update_bounding_box_data(bounds_arr, seg_remapped)

time_elapsed = time.time() - start_time
logging.info("Frame {} finished in {:5.2f} seconds.".format(int(frame_number), time_elapsed))
logging.info(
"Frame {} finished in {:5.2f} seconds.".format(int(frame_number), time_elapsed)
)


def make_all_frames(
Expand Down Expand Up @@ -399,7 +445,9 @@ def make_features(
for feature in features:
if feature.column_name not in dataset.columns:
logging.warning(
"Feature '{}' not found in dataset. Skipping...".format(feature.column_name)
"Feature '{}' not found in dataset. Skipping...".format(
feature.column_name
)
)
continue

Expand All @@ -408,7 +456,7 @@ def make_features(
dataset=dataset_name,
colorizer=True,
)

# Remove parentheses from unit names, if included.
if len(unit) >= 2 and unit[0] == "(" and unit[-1] == ")":
unit = unit[1:-1]
Expand All @@ -418,12 +466,18 @@ def make_features(
# Get data and scale to use actual units
if scale_factor is not None:
data = data * scale_factor
description = GLOSSARY[feature.column_name]

description = GLOSSARY.get(feature.column_name, "")

writer.write_feature(
data,
FeatureInfo(label=label, unit=unit, type=feature.type, categories=feature.categories, description=description),
FeatureInfo(
label=label,
unit=unit,
type=feature.type,
categories=feature.categories,
description=description,
),
outliers=outliers,
)

Expand All @@ -447,6 +501,7 @@ def make_dataset(
do_frames=True,
scale=0.25,
parallel=False,
make_backdrops=True,
):
"""Make a new dataset from the given data, and write the complete dataset
files to the given output directory.
Expand Down Expand Up @@ -515,8 +570,19 @@ def make_dataset(
writer.set_frame_paths(generate_frame_paths(nframes))

make_features(full_dataset, FEATURE_COLUMNS[filter], dataset, writer)

if do_frames:
make_all_frames(grouped_frames, scale, writer, parallel)

if make_backdrops:
save_colony_backdrop_mips(
dataset, output_dir_subset + f"/{dataset}/backdrops/"
)
backdrop_paths = [f"./backdrops/{i}.png" for i in range(nframes)]
writer.add_backdrops(
"Max intensity z-projection of Lamin B1", backdrop_paths
)

writer.write_manifest(metadata=metadata)


Expand Down Expand Up @@ -558,6 +624,12 @@ def make_dataset(
"Has no effect with --noframes.",
)

parser.add_argument(
"--make_backdrops",
type=bool,
default=True,
help="True will generate backdrops (Default). False will use previously generated backdrops or display none if they have not been generated before.",
)
args = parser.parse_args()


Expand All @@ -572,6 +644,7 @@ def main():
do_frames=not args.noframes,
scale=args.scale,
parallel=args.parallel,
make_backdrops=args.make_backdrops,
)


Expand Down
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