From e8461666465249eb505f21a0375d4eba537ddb65 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Nov 2024 07:06:48 +0100
Subject: [PATCH] .to_8bit was causing problems when applied to an accessor
that was already 8-bt
---
model_server/base/accessors.py | 5 ++++-
model_server/base/roiset.py | 8 ++++++--
2 files changed, 10 insertions(+), 3 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 49666cfe..7e7affa1 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -205,7 +205,10 @@ class GenericImageDataAccessor(ABC):
)
def to_8bit(self):
- return self.apply(resample_to_8bit, preserve_dtype=False)
+ if self.dtype == 'uint8':
+ return self
+ else:
+ return self.apply(resample_to_8bit, preserve_dtype=False)
class InMemoryDataAccessor(GenericImageDataAccessor):
def __init__(self, data):
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 13ca95b7..e11450aa 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -63,6 +63,7 @@ class RoiSetExportParams(BaseModel):
class RoiSetLabelsOverlayParams(BaseModel):
transparency: float = 0.5
mip: bool = False
+ rescale_clip: Union[float, None] = None
patches_3d: Union[PatchParams, None] = None
annotated_patches_2d: Union[PatchParams, None] = None
patches_2d: Union[PatchParams, None] = None
@@ -688,8 +689,12 @@ class RoiSet(object):
white_channel,
transparency: float = 0.5,
mip: bool = False,
+ rescale_clip: Union[float, None] = None,
) -> InMemoryDataAccessor:
- mono = self.acc_raw.get_mono(channel=white_channel).to_8bit().data_yxz
+ mono = self.acc_raw.get_mono(channel=white_channel)
+ if rescale_clip is not None:
+ mono = mono.apply(lambda x: rescale(x, clip=rescale_clip))
+ mono = mono.to_8bit().data_yxz
max_label = self.get_df()['label'].max()
palette = np.array([[0, 0, 0]] + glasbey.create_palette(max_label, as_hex=False))
rgb_8bit_palette = (255 * palette).round().astype('uint8')
@@ -699,7 +704,6 @@ class RoiSet(object):
[0, 1, 3, 2],
[0, 1, 2, 3]
)
-
combined = np.stack([mono, mono, mono], axis=2) + (1.0 - transparency) * id_map_yxcz
combined_8bit = np.clip(combined, 0, 255).round().astype('uint8')
--
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