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Add a progress bar for mssr (GUI + terminal) #3

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Add a progress bar for mssr (GUI + terminal) #3

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1 change: 1 addition & 0 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ packages = find:
install_requires =
matplotlib
numba
numba-progress
numpy
magicgui
qtpy
Expand Down
40 changes: 32 additions & 8 deletions src/lnma_superres/core_mssr_numba.py
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Original file line number Diff line number Diff line change
@@ -1,29 +1,36 @@
import math

import napari.utils
import numba
import numba.cuda
import numba_progress
import numpy as np
import math
import scipy.interpolate as interpolate


@numba.njit(parallel=True)
def cpu_max_diff(img: np.ndarray, hs: int) -> np.ndarray:
def cpu_max_diff(img: np.ndarray, hs: int, progress_proxy=None) -> np.ndarray:
height, width = img.shape
max_diff = np.zeros((height, width))
for i in numba.prange(height):
for j in numba.prange(width):
max_diff[i, j] = np.max(np.abs(img[max(i - hs, 0) : i + hs + 1, max(j - hs, 0) : j + hs + 1] - img[i, j]))
if progress_proxy is not None:
progress_proxy.update(width)
return max_diff


@numba.njit(parallel=True)
def cpu_mean_shift(padded: np.ndarray, hs: int, max_diff: np.ndarray, kernel: np.ndarray) -> np.ndarray:
def cpu_mean_shift(padded: np.ndarray, hs: int, max_diff: np.ndarray, kernel: np.ndarray, progress_proxy=None) -> np.ndarray:
height, width = padded.shape
y = np.zeros((height - 2 * hs, width - 2 * hs), dtype=np.float64)
for i in numba.prange(height - 2 * hs):
for j in numba.prange(width - 2 * hs):
window = padded[i : i + 2 * hs + 1, j : j + 2 * hs + 1]
weights = np.exp(-(((window - padded[i + hs, j + hs]) / max_diff[i, j]) ** 2)) * kernel
y[i, j] = (window * weights).sum() / weights.sum()
if progress_proxy is not None:
progress_proxy.update(width)

return y

Expand Down Expand Up @@ -70,7 +77,6 @@ def cuda_mean_shift(padded: np.ndarray, hs: int, max_diff: np.ndarray, kernel: n
output[i, j] = cum_value / cum_weight



class mssr_class:
def __init__(self):
self.first = "init"
Expand Down Expand Up @@ -134,6 +140,8 @@ def meshing(self,img, amp):

# Spatial MSSR
def sfMSSR(self, img, fwhm, amp, order, mesh=True, ftI=False, intNorm=True, device="cuda"):
napari_progress = napari.utils.progress(total=10)
napari_progress.set_description("Interpolate")
assert device in ("cpu", "cuda")

if device == "cuda" and not numba.cuda.is_available():
Expand All @@ -152,16 +160,25 @@ def sfMSSR(self, img, fwhm, amp, order, mesh=True, ftI=False, intNorm=True, devi
elif amp > 1 and ftI:
img = self.ftInterp(img, amp, mesh)

napari_progress.update(2)
napari_progress.set_description("Max diff")

i = np.arange(-hs, hs + 1)
j = np.arange(-hs, hs + 1)
kernel = np.exp(-(i[None] ** 2 + j[:, None] ** 2) / hs**2)
kernel[hs, hs] = 0


if device == "cpu":
max_diff = cpu_max_diff(img, hs)
max_diff[max_diff == 0] = 1 # Prevent 0 division
MS = img - cpu_mean_shift(np.pad(img, hs, "symmetric"), hs, max_diff, kernel)
with numba_progress.ProgressBar(total=img.size, desc="Max Diff", leave=False) as progress_proxy:
max_diff = cpu_max_diff(img, hs, progress_proxy)
max_diff[max_diff == 0] = 1 # Prevent 0 division

napari_progress.update(3)
napari_progress.set_description("Mean Shift")
with numba_progress.ProgressBar(total=img.size, desc="Mean Shift", leave=False) as progress_proxy:
MS = img - cpu_mean_shift(np.pad(img, hs, "symmetric"), hs, max_diff, kernel, progress_proxy)
napari_progress.update(5)
napari_progress.set_description("MSSR")
else:
max_tpb = numba.cuda.get_current_device().MAX_THREADS_PER_BLOCK
max_tpb = 20
Expand All @@ -171,6 +188,9 @@ def sfMSSR(self, img, fwhm, amp, order, mesh=True, ftI=False, intNorm=True, devi
max_diff = numba.cuda.device_array_like(img)
output = numba.cuda.device_array_like(img)
cuda_max_diff[blocks, (tpb, tpb)](numba.cuda.to_device(img), hs, max_diff)

napari_progress.update(3)
napari_progress.set_description("Mean Shift")
cuda_mean_shift[blocks, (tpb, tpb)](
numba.cuda.to_device(np.pad(img, hs, "symmetric")),
hs,
Expand All @@ -179,6 +199,8 @@ def sfMSSR(self, img, fwhm, amp, order, mesh=True, ftI=False, intNorm=True, devi
output,
)
MS = img - output
napari_progress.update(5)
napari_progress.set_description("MSSR")

MS[MS < 0] = 0
I3 = MS / MS.max()
Expand All @@ -196,6 +218,8 @@ def sfMSSR(self, img, fwhm, amp, order, mesh=True, ftI=False, intNorm=True, devi
IMSSR = I3 * img
else:
IMSSR = I3

napari_progress.close()
return IMSSR

#Temporal MSSR
Expand Down
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