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set contiguous array before conversion from array to tensor #114

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set contiguous array before conversion from array to tensor #114

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ZhengguoTan
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@sidward
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sidward commented Jul 26, 2022 •
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Thanks for the pull request. Current the requirements.txt file enforces the numpy version to be <=1.20 while the numpy docs state that ascontiguousarray is new from 1.20 onwards.

I am planning to upgrade the underlying packages as soon as I have time, as there are a lot of old dependencies. I will leave this open for now, and merge it after I've done the same.

@ZhengguoTan
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Thanks for the pull request. Current the requirements.txt file enforces the numpy version to be <=1.20 while the numpy docs state that ascontiguousarray is new from 1.20 onwards.

I am planning to upgrade the underlying packages as soon as I have time, as there are a lot of old dependencies. I will leave this open for now, and merge it after I've done the same.

Thanks for the quick reply. Look forward to contributing to this package.

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sidward commented May 27, 2023

Hi @ZhengguoTan I just pushed some tooling that cleaned the code. Can you make your changes after the changes on main?

@ZhengguoTan
set contiguous array before conversion from array to tensor
49ba42e
@ZhengguoTan
remove warning when using sigpy on cpu with cupy installed
ba61c83
@ZhengguoTan
set contiguous array when not c_contiguous
b38aad7
@ZhengguoTan
add keepdims option in rss
509fb39
@ZhengguoTan
add symm option in hanning function: allows for symmetric hanning window
2af4f2e
@ZhengguoTan
add verbose option in ConjugateGradient
38d308f
@ZhengguoTan
add keepdims option in Sum and Tile linop
2deb39b
@ZhengguoTan
use 'mean' option to handle overlapping local blocks
0fda946
@ZhengguoTan
allow for the use of device in Slice linop
a26a3c4
@ZhengguoTan
add Sobolev linop
a176772
@ZhengguoTan
add HDNUFFT linop for high-dimensional NUFFT
57dceb8 
* e.g. multi-temporal-frame NUFFT
@ZhengguoTan
test Conjugate of prox operators
ffc87e8
@ZhengguoTan
bump up to NumPy 1.20 and Torch 1.12
3c93af3
@ZhengguoTan
allow for scaling in LinearLeastSquares
6e41588
@ZhengguoTan
make sure all arrays are on the same device in LinearLeastSquares
5f4d023
@ZhengguoTan
allow for verbose in LinearLeastSquares
a99ca8e
@ZhengguoTan
nlop: a generalized nonlinear operator framework
40ff409 
* Exponential: nonlinear exponential class
* Compose: allows for the chain from nlop to linop
@ZhengguoTan
add iteratively regularized Gauss-Newton method (IRGNM) algorithm
a00607c
@ZhengguoTan
add NonlinearLeastSquares App
5b1ce4c 
This app solves nonlinear inverse problem;
A demo for solving the exponential function is provided in tests/test_app.py
@ZhengguoTan
Nlinv: parallel imaging as a nonlinear operator
4120785
@ZhengguoTan
add a test case of model-based DTI reconstruction
cf5d90c
@ZhengguoTan
coding style
fd45a5a
@ZhengguoTan
coord: conversion between Cartesian and Spherical coordinates
c35e056
@ZhengguoTan
epi: module for diffusion MRI based on EPI
9b5d30d 
* odd/even echo phase correction
* construction of diffusion encoding matrix
* DTI/DKI model fitting
@ZhengguoTan
retro: module for performing retrospective undersampling in EPI
6d40f6e
@ZhengguoTan
sms: module for Simultaneous Multi-Slice
47d203b 
* Siemens:
  + reorder reconstructed slices in the correct geometric order
  + compute FOV phase shift in the ky direction

* readout extended FOV methods
@ZhengguoTan
coding style
b4fb22f
@ZhengguoTan
verbose in alg
01df496
@ZhengguoTan
allow for single paramter setting in muse denoising
7d48c6e
@ZhengguoTan
unit in test_dce
866244c
@ZhengguoTan
new test case in sms
7fc9f31
@ZhengguoTan
coil compression (cc) module
80e05b0
@ZhengguoTan
diffusion vector set (dvs) module
5d33c7d
@ZhengguoTan
rename app
10d93cd
@ZhengguoTan
fix import
0066f7e
@ZhengguoTan
add normalization option in LLRL1Reg: enables singular value normaliz…
a8dda98 
…ation
@ZhengguoTan
checkin an install.sh script that works in conda
8c2f996
@ZhengguoTan
specify python 3.10 version
56a90a2
@ZhengguoTan
set verbose default as False in muse
74b94ff
@ZhengguoTan
use antialias in Resize
3cbcd6f
@ZhengguoTan
reorder slices incl. sms = 3
158e740
@ZhengguoTan
add RealValueConstraint linop
5700540
@ZhengguoTan
use RealValueConstraint in MUSE
a6cb399
@ZhengguoTan
dicom module
24bdfa0
@ZhengguoTan
update sense linop to allow up highdims and chain with nlop
598619b
@ZhengguoTan
numpy version bump
5b0b2a6
@ZhengguoTan
add dti nlop
000add8
@ZhengguoTan
add nlls and nlrecon
0413065
@ZhengguoTan
add model-based dti recon app
50b9d24
@ZhengguoTan
add diff module
9ef850c
@ZhengguoTan
add gmap and grappa modules
9f5a0cc 
* gmap: pseudo replica to produce g-factor map
* grappa: 2D grappa and slice grappa
@ZhengguoTan
remove redundant lines
34d2ed9
@ZhengguoTan
reformat test epi
bbc0d5e
@ZhengguoTan
test coord
a9cd8be
@ZhengguoTan
torch_dce module
99a2f4d
@ZhengguoTan
ADC calculation
fe0b9ef
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@ZhengguoTan @sidward