From a3736cc950c9b0089670e59e6ae9f85d8d9c7592 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 6 Feb 2025 09:49:05 +0100
Subject: [PATCH] read CSVs via a utility method
---
model_server/base/api.py | 1 -
model_server/base/roiset.py | 6 ++++--
tests/base/test_roiset.py | 6 +++---
3 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/model_server/base/api.py b/model_server/base/api.py
index 9c69038c..3549633d 100644
--- a/model_server/base/api.py
+++ b/model_server/base/api.py
@@ -262,5 +262,4 @@ def list_tasks() -> Dict[str, TaskInfo]:
@app.get('/phenobase/bounding_box')
def get_phenobase_bounding_boxes() -> list:
- # TODO: exception when casting this as list
return session.phenobase.list_bounding_boxes()
\ No newline at end of file
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 696922b9..244acc65 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -489,6 +489,9 @@ def insert_level(df: pd.DataFrame, name: str):
],
)
+def read_roiset_df(csv_path: Path) -> pd.DataFrame:
+ return pd.read_csv(csv_path, header=[0, 1], index_col=0)
+
class RoiSet(object):
@@ -1287,7 +1290,6 @@ class RoiSet(object):
def acc_obj_ids(self):
return make_object_ids_from_df(self._df, self.acc_raw.shape_dict)
- # TODO: move to dedicated CSV reader in tests and scripts
@classmethod
def deserialize(cls, acc_raw: GenericImageDataAccessor, where: Path, prefix='roiset') -> Self:
@@ -1299,7 +1301,7 @@ class RoiSet(object):
:param prefix: starting prefix of patch mask filenames
:return: RoiSet object
"""
- df = pd.read_csv(where / 'dataframe' / (prefix + '.csv'), header=[0, 1], index_col=0)
+ df = read_roiset_df(where / 'dataframe' / (prefix + '.csv'))
df.index.name = 'label'
pa_masks = where / 'tight_patch_masks'
is_3d = is_df_3d(df)
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 07acffa5..fc017505 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -7,7 +7,7 @@ from pathlib import Path
import pandas as pd
from model_server.base.process import smooth
-from model_server.base.roiset import filter_df_overlap_bbox, filter_df_overlap_seg, IntensityThresholdInstanceMaskSegmentationModel, RoiSet, RoiSetExportParams, RoiSetMetaParams
+from model_server.base.roiset import filter_df_overlap_bbox, filter_df_overlap_seg, IntensityThresholdInstanceMaskSegmentationModel, read_roiset_df, RoiSet, RoiSetExportParams, RoiSetMetaParams
from model_server.base.accessors import generate_file_accessor, InMemoryDataAccessor, PatchStack, write_accessor_data_to_file
import model_server.conf.testing as conf
from model_server.conf.testing import DummyInstanceMaskSegmentationModel
@@ -661,7 +661,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertTrue((where / v).exists())
# test on paths in CSV
- test_df = pd.read_csv(where / res['dataframe'], header=[0, 1], index_col=0)
+ test_df = read_roiset_df(where / res['dataframe'])
for c in ['tight_patch_masks_path', 'patches_2d_path', 'patches_2d_annotated_path']:
self.assertTrue(c in test_df.patches.columns)
for f in test_df.patches[c]:
@@ -818,7 +818,7 @@ class TestRoiSetSerialization(unittest.TestCase):
ref_roiset.serialize(where_ser, prefix='ref')
where_df = where_ser / 'dataframe' / 'ref.csv'
self.assertTrue(where_df.exists())
- df_test = pd.read_csv(where_df, header=[0, 1], index_col=0)
+ df_test = read_roiset_df(where_df)
# check that patches are correct size
where_patch_masks = where_ser / 'tight_patch_masks'
--
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