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Add option to export to CSV via sleap-convert and API #1730

Merged
merged 15 commits into from
Apr 9, 2024
Merged

Add option to export to CSV via sleap-convert and API #1730

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db7f3d4
Add csv as a format option
eberrigan Mar 21, 2024
3ecc99a
Add analysis to format
eberrigan Mar 21, 2024
c4fb39e
Add csv suffix to output path
eberrigan Mar 21, 2024
c998d3d
Add condition for csv analysis file
eberrigan Mar 21, 2024
d2b658c
Add export function to Labels class
eberrigan Mar 21, 2024
0b51fea
Merge branch 'develop' into elizabeth/add-option-to-export-to-csv
eberrigan Apr 3, 2024
85d122c
Merge branch 'develop' into elizabeth/add-option-to-export-to-csv
talmo Apr 8, 2024
9eb4270
Merge branch 'develop' into elizabeth/add-option-to-export-to-csv
talmo Apr 8, 2024
ff7ee51
delete print statement
eberrigan Apr 8, 2024
f7929a2
lint
eberrigan Apr 8, 2024
821d114
Add `analysis.csv` as parametrize input for `sleap-convert` tests
eberrigan Apr 8, 2024
3eeb9fd
test `export_csv` method added to `Labels` class
eberrigan Apr 8, 2024
b4bdca1
black formatting
eberrigan Apr 8, 2024
79d0654
use `Path` to construct filename
eberrigan Apr 8, 2024
e508587
add `analysis.csv` to cli guide for `sleap-convert`
eberrigan Apr 8, 2024
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23 changes: 22 additions & 1 deletion sleap/io/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@ def create_parser():
help="Output format. Default ('slp') is SLEAP dataset; "
"'analysis' results in analysis.h5 file; "
"'analysis.nix' results in an analysis nix file;"
"'analysis.csv' results in an analysis csv file;"
"'h5' or 'json' results in SLEAP dataset "
"with specified file format.",
)
Expand Down Expand Up @@ -105,6 +106,7 @@ def main(args: list = None):
"""
parser = create_parser()
args = parser.parse_args(args=args)
print(args)
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Remove the debug print statement to maintain a clean and professional codebase.

-    print(args)
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
print(args)


video_callback = Labels.make_video_callback([os.path.dirname(args.input_path)])
try:
Expand Down Expand Up @@ -135,7 +137,12 @@ def main(args: list = None):
outnames = [path for path in args.outputs]
if len(outnames) < len(vids):
# if there are less outnames provided than videos to convert...
out_suffix = "nix" if "nix" in args.format else "h5"
if "nix" in args.format:
out_suffix = "nix"
elif "csv" in args.format:
out_suffix = "csv"
else:
out_suffix = "h5"
Comment on lines +139 to +144
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Refactor the logic for determining the output file suffix into a separate function to improve code readability and maintainability.

+ def determine_output_suffix(format_arg: str) -> str:
+     if "nix" in format_arg:
+         return "nix"
+     elif "csv" in format_arg:
+         return "csv"
+     else:
+         return "h5"
- if "nix" in args.format:
-     out_suffix = "nix"
- elif "csv" in args.format:
-     out_suffix = "csv"
- else:
-     out_suffix = "h5"
+ out_suffix = determine_output_suffix(args.format)
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
if "nix" in args.format:
out_suffix = "nix"
elif "csv" in args.format:
out_suffix = "csv"
else:
out_suffix = "h5"
def determine_output_suffix(format_arg: str) -> str:
if "nix" in format_arg:
return "nix"
elif "csv" in format_arg:
return "csv"
else:
return "h5"
out_suffix = determine_output_suffix(args.format)

fn = args.input_path
fn = re.sub("(\.json(\.zip)?|\.h5|\.slp)$", "", fn)
fn = PurePath(fn)
Expand All @@ -158,6 +165,20 @@ def main(args: list = None):
NixAdaptor.write(outname, labels, args.input_path, video)
except ValueError as e:
print(e.args[0])

elif "csv" in args.format:
from sleap.info.write_tracking_h5 import main as write_analysis

for video, output_path in zip(vids, outnames):
write_analysis(
labels,
output_path=output_path,
labels_path=args.input_path,
all_frames=True,
video=video,
csv=True,
)

else:
from sleap.info.write_tracking_h5 import main as write_analysis

Expand Down
15 changes: 15 additions & 0 deletions sleap/io/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2055,6 +2055,21 @@ def export(self, filename: str):

SleapAnalysisAdaptor.write(filename, self)


def export_csv(self, filename: str):
"""Export labels to CSV format.

Args:
filename: Output path for the CSV format file.

Notes:
This will write the contents of the labels out as a CSV file.
"""
from sleap.io.format.csv import CSVAdaptor

CSVAdaptor.write(filename, self)
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def export_nwb(
self,
filename: str,
Expand Down
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