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BUG: Allow types np.integer and np.floating #127

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Merged
Leengit merged 1 commit into from
Apr 21, 2023
Merged

BUG: Allow types np.integer and np.floating #127

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50 changes: 32 additions & 18 deletions histomics_stream/configure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,8 @@ def __init__(self, study, target_magnification, magnification_source):
if not ("version" in study and study["version"] == "version-1"):
raise ValueError('study["version"] must exist and be equal to "version-1".')
if not (
isinstance(target_magnification, (int, float)) and 0 < target_magnification
isinstance(target_magnification, (int, np.integer, float, np.floating))
and 0 < target_magnification
):
raise ValueError(
f"target_magnification ({target_magnification})"
Expand Down Expand Up @@ -453,34 +454,40 @@ def __init__(self, study, **kwargs):
raise ValueError('study["version"] must exist and be equal to "version-1".')
if not (
"tile_height" in study
and isinstance(study["tile_height"], int)
and isinstance(study["tile_height"], (int, np.integer))
and study["tile_height"] > 0
):
raise ValueError(
'study["tile_height"]' " must exist and be a positive integer"
)
if not (
"tile_width" in study
and isinstance(study["tile_width"], int)
and isinstance(study["tile_width"], (int, np.integer))
and study["tile_width"] > 0
):
raise ValueError(
'study["tile_width"]' " must exist and be a positive integer"
)
if not (isinstance(randomly_select, int) and -1 <= randomly_select):
if not (
isinstance(randomly_select, (int, np.integer)) and -1 <= randomly_select
):
raise ValueError(
f"randomly_select ({randomly_select})"
" must be a non-negative integer or -1."
)
if not (
isinstance(overlap_height, int) and overlap_height < study["tile_height"]
isinstance(overlap_height, (int, np.integer))
and overlap_height < study["tile_height"]
):
raise ValueError(
f"overlap_height ({overlap_height})"
" must be less than"
f' tile_height ({study["tile_height"]}).'
)
if not (isinstance(overlap_width, int) and overlap_width < study["tile_width"]):
if not (
isinstance(overlap_width, (int, np.integer))
and overlap_width < study["tile_width"]
):
raise ValueError(
f"overlap_width ({overlap_width})"
" must be less than"
Expand All @@ -489,7 +496,7 @@ def __init__(self, study, **kwargs):
if mask_filename != "":
mask_itk = self.check_mask_filename(mask_filename)
if not (
isinstance(mask_threshold, float)
isinstance(mask_threshold, (float, np.floating))
and mask_threshold >= 0.0
and mask_threshold <= 1.0
):
Expand Down Expand Up @@ -717,21 +724,23 @@ def __init__(self, study, randomly_select=-1, tiles_dictionary={}):
raise ValueError('study["version"] must exist and be equal to "version-1".')
if not (
"tile_height" in study
and isinstance(study["tile_height"], int)
and isinstance(study["tile_height"], (int, np.integer))
and study["tile_height"] > 0
):
raise ValueError(
'study["tile_height"]' " must exist and be a positive integer"
)
if not (
"tile_width" in study
and isinstance(study["tile_width"], int)
and isinstance(study["tile_width"], (int, np.integer))
and study["tile_width"] > 0
):
raise ValueError(
'study["tile_width"]' " must exist and be a positive integer"
)
if not (isinstance(randomly_select, int) and -1 <= randomly_select):
if not (
isinstance(randomly_select, (int, np.integer)) and -1 <= randomly_select
):
raise ValueError(
f"randomly_select ({randomly_select})"
" must be a non-negative integer or -1."
Expand Down Expand Up @@ -832,21 +841,23 @@ def __init__(self, study, randomly_select=1): # Defaults to select one
raise ValueError('study["version"] must exist and be equal to "version-1".')
if not (
"tile_height" in study
and isinstance(study["tile_height"], int)
and isinstance(study["tile_height"], (int, np.integer))
and study["tile_height"] > 0
):
raise ValueError(
'study["tile_height"]' " must exist and be a positive integer"
)
if not (
"tile_width" in study
and isinstance(study["tile_width"], int)
and isinstance(study["tile_width"], (int, np.integer))
and study["tile_width"] > 0
):
raise ValueError(
'study["tile_width"]' " must exist and be a positive integer"
)
if not (isinstance(randomly_select, int) and 0 <= randomly_select):
if not (
isinstance(randomly_select, (int, np.integer)) and 0 <= randomly_select
):
raise ValueError(
f"randomly_select ({randomly_select})"
" must be a non-negative integer."
Expand Down Expand Up @@ -904,7 +915,7 @@ def __call__(self, study_description):
)
if not (
"tile_height" in study_description
and isinstance(study_description["tile_height"], int)
and isinstance(study_description["tile_height"], (int, np.integer))
and study_description["tile_height"] > 0
):
raise ValueError(
Expand All @@ -913,7 +924,7 @@ def __call__(self, study_description):
)
if not (
"tile_width" in study_description
and isinstance(study_description["tile_width"], int)
and isinstance(study_description["tile_width"], (int, np.integer))
and study_description["tile_width"] > 0
):
raise ValueError(
Expand All @@ -926,7 +937,10 @@ def __call__(self, study_description):

if not (
"returned_magnification" in slide
and isinstance(slide["returned_magnification"], (int, float))
and isinstance(
slide["returned_magnification"],
(int, np.integer, float, np.floating),
)
and slide["returned_magnification"] > 0
):
raise ValueError(
Expand Down Expand Up @@ -957,15 +971,15 @@ def _designate_chunks_for_tiles(self, study_description):

if not (
"chunk_height" in slide
and isinstance(slide["chunk_height"], int)
and isinstance(slide["chunk_height"], (int, np.integer))
and slide["chunk_height"] > 0
):
raise ValueError(
'slide["chunk_height"]' " must exist and be a positive integer"
)
if not (
"chunk_width" in slide
and isinstance(slide["chunk_width"], int)
and isinstance(slide["chunk_width"], (int, np.integer))
and slide["chunk_width"] > 0
):
raise ValueError(
Expand Down