feat: add cropping methods from FMCIB pipeline

config/ruff.toml

@@ -7,7 +7,8 @@ include = [
   "src/readii/cli/**/*.py",
   "src/readii/negative_controls_refactor/**.py",
   "src/readii/io/**/**.py",
-  "src/readii/analyze/**.py"
+  "src/readii/analyze/**.py",
+  "src/readii/process/**.py"
 ]
 
 # extend-exclude is used to exclude directories from the flake8 checks

src/readii/process/__init__.py

@@ -0,0 +1,35 @@
+"""Module for processing and manipulating data."""
+
+from .label import (
+    addOutcomeLabels,
+    convertDaysToYears,
+    eventOutcomeColumnSetup,
+    getPatientIdentifierLabel,
+    setPatientIdAsIndex,
+    survivalStatusToNumericMapping,
+    timeOutcomeColumnSetup,
+)
+from .select import (
+    dropUpToFeature,
+    getOnlyPyradiomicsFeatures,
+    selectByColumnValue,
+)
+from .split import (
+    replaceColumnValues,
+    splitDataByColumnValue,
+)
+
+__all__ = [
+    "addOutcomeLabels",
+    "convertDaysToYears",
+    "getPatientIdentifierLabel",
+    "setPatientIdAsIndex",
+    "timeOutcomeColumnSetup",
+    "survivalStatusToNumericMapping",
+    "eventOutcomeColumnSetup",
+    "replaceColumnValues",
+    "splitDataByColumnValue",
+    "dropUpToFeature",
+    "selectByColumnValue",
+    "getOnlyPyradiomicsFeatures",
+]

src/readii/process/images/__init__.py

@@ -0,0 +1,25 @@
+"""Module for processing and manipulating images."""
+
+from .crop import (
+    apply_bounding_box_limits,
+    check_bounding_box_single_dimension,
+    crop_image_to_mask,
+    crop_to_bounding_box,
+    crop_to_centroid,
+    crop_to_maxdim_cube,
+    find_bounding_box,
+    find_centroid,
+    validate_new_dimensions,
+)
+
+__all__ = [
+    "crop_image_to_mask",
+    "find_bounding_box",
+    "find_centroid",
+    "validate_new_dimensions",
+    "apply_bounding_box_limits",
+    "check_bounding_box_single_dimension",
+    "crop_to_maxdim_cube",
+    "crop_to_bounding_box",
+    "crop_to_centroid",
+]