From 9dd88f7ee45424a47ae173d6be9bb7b0550a4b90 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 29 Sep 2023 11:04:38 +0200
Subject: [PATCH] Consolidated utility methods and added tests for 2, 3, 4
dimension padding
---
model_server/process.py | 52 ++++++++++++++++++++++++-----------------
tests/test_process.py | 30 ++++++++++++++++++++++++
2 files changed, 61 insertions(+), 21 deletions(-)
create mode 100644 tests/test_process.py
diff --git a/model_server/process.py b/model_server/process.py
index 26fd3005..2bc09422 100644
--- a/model_server/process.py
+++ b/model_server/process.py
@@ -6,38 +6,42 @@ from math import ceil, floor
import numpy as np
from skimage.exposure import rescale_intensity
-
-def pad(im, mpx): # now in model_server.batch
- '''Pads and crops image width edge values to specified dimension'''
- dh = 0.5 * (mpx - im.shape[0])
- dw = 0.5 * (mpx - im.shape[1])
+def pad(yxcz, mpx: int):
+ """
+ Pad and crop image data in Y and X axes to meet specific dimension
+ :param yxcz: np.ndarray
+ :param mpx: int pixel size of resulting square
+ :return: np.ndarray array of size (mpx, mpx, nc, nz)
+ """
+ assert len(yxcz.shape) == 4
+ nc = yxcz.shape[2]
+ nz = yxcz.shape[3]
+ dh = 0.5 * (mpx - yxcz.shape[0])
+ dw = 0.5 * (mpx - yxcz.shape[1])
if dw < 0:
x0 = floor(-dw)
x1 = x0 + mpx
- im = im[:, x0:x1]
+ yxcz = yxcz[:, x0:x1, :, :]
dw = 0
if dh < 0:
y0 = floor(-dh)
y1 = y0 + mpx
- im = im[y0:y1, :]
+ yxcz = yxcz[y0:y1, :, :, :]
dh = 0
- border = ((floor(dh), ceil(dh)), (floor(dw), ceil(dw)))
- padded = np.pad(im, border, mode='constant')
- if padded.shape != (mpx, mpx):
- raise Exception(f'Incorrect image shape: {padded.shape} v. {(mpx, mpx)}')
- return padded
-
-def pad_3d(im, mpx): # im: [z x h x w]
- assert(len(im.shape) == 3)
- nz, h, w = im.shape
- padded = np.zeros((nz, mpx, mpx), dtype=im.dtype)
- for zi in range(nz):
- padded[zi, :, :] = pad(im[zi, :, :], mpx)
+ border = ((floor(dh), ceil(dh)), (floor(dw), ceil(dw)), (0, 0), (0, 0))
+ padded = np.pad(yxcz, border, mode='constant')
return padded
-def resample(nda, cmin=0, cmax=2**16): # now in model_server.batch
+def resample_to_8bit(nda, cmin=0, cmax=2**16):
+ """
+ Resample a 16 bit image to 8 bit, optionally bracketing a given intensity range
+ :param nda: np.ndarray input data of arbitrary dimension
+ :param cmin: intensity level on 16-bit scale that become zero in 8-bit scale
+ :param cmax: intensity level on 16-bit scale that become maximum (255) in 8-bit scale
+ :return: rescaled data of same dimension as input
+ """
return rescale_intensity(
np.clip(nda, cmin, cmax),
in_range=(cmin, cmax + 1),
@@ -45,7 +49,13 @@ def resample(nda, cmin=0, cmax=2**16): # now in model_server.batch
).astype('uint8')
-def rescale(nda, clip=0.0): # now in model_server.batch
+def rescale(nda, clip=0.0):
+ """
+ Rescale an image for a given clipping ratio
+ :param nda: input data of arbitrary dimension and scale
+ :param clip: Ratio of clipping in the resulting image
+ :return: rescaled image of same dimension as input
+ """
clip_pct = (100.0 * clip, 100.0 * (1.0 - clip))
cmin, cmax = np.percentile(nda, clip_pct)
rescaled = rescale_intensity(nda, in_range=(cmin, cmax))
diff --git a/tests/test_process.py b/tests/test_process.py
new file mode 100644
index 00000000..bef8426e
--- /dev/null
+++ b/tests/test_process.py
@@ -0,0 +1,30 @@
+import unittest
+
+import numpy as np
+
+from model_server.process import pad
+
+class TestProcessingUtilityMethods(unittest.TestCase):
+ def setUp(self) -> None:
+ w = 200
+ h = 300
+ nc = 4
+ nz = 11
+ self.data2d = (2**16 * np.random.rand(h, w, 1, 1)).astype('uint16')
+ self.data3d = (2**16 * np.random.rand(h, w, 1, nz)).astype('uint16')
+ self.data4d = (2**16 * np.random.rand(h, w, nc, nz)).astype('uint16')
+
+ def test_pad_2d(self):
+ padded = pad(self.data2d, 256)
+ self.assertEqual(padded.shape, (256, 256, 1, 1))
+
+ def test_pad_3d(self):
+ nz = self.data3d.shape[3]
+ padded = pad(self.data3d, 256)
+ self.assertEqual(padded.shape, (256, 256, 1, nz))
+
+ def test_pad_4d(self):
+ nc = self.data4d.shape[2]
+ nz = self.data4d.shape[3]
+ padded = pad(self.data4d, 256)
+ self.assertEqual(padded.shape, (256, 256, nc, nz))
\ No newline at end of file
--
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