2022-04-08T11:11:25,341 Created temporary directory: /tmp/pip-ephem-wheel-cache-clxop7xu
2022-04-08T11:11:25,347 Created temporary directory: /tmp/pip-req-tracker-xtm8fgqm
2022-04-08T11:11:25,348 Initialized build tracking at /tmp/pip-req-tracker-xtm8fgqm
2022-04-08T11:11:25,348 Created build tracker: /tmp/pip-req-tracker-xtm8fgqm
2022-04-08T11:11:25,348 Entered build tracker: /tmp/pip-req-tracker-xtm8fgqm
2022-04-08T11:11:25,350 Created temporary directory: /tmp/pip-wheel-qrnv_8wt
2022-04-08T11:11:25,418 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-04-08T11:11:25,426 2 location(s) to search for versions of mdreg:
2022-04-08T11:11:25,426 * https://pypi.org/simple/mdreg/
2022-04-08T11:11:25,426 * https://www.piwheels.org/simple/mdreg/
2022-04-08T11:11:25,428 Fetching project page and analyzing links: https://pypi.org/simple/mdreg/
2022-04-08T11:11:25,429 Getting page https://pypi.org/simple/mdreg/
2022-04-08T11:11:25,432 Found index url https://pypi.org/simple
2022-04-08T11:11:25,541   Skipping link: No binaries permitted for mdreg: https://files.pythonhosted.org/packages/bc/10/c83070f17306c03d644c7c76d8859872032edc1fc0df2a97380d4e93d708/mdreg-0.3.0-py3-none-any.whl#sha256=76d01b7c8b72d51decaaa5d64f040e8eb72037e15e17105cf8d1a84546559e46 (from https://pypi.org/simple/mdreg/) (requires-python:>=3.6, <4)
2022-04-08T11:11:25,543   Found link https://files.pythonhosted.org/packages/78/c8/ba73412c97b1eedd387919d54687fb19b22173a3ba98a9a77136320259eb/mdreg-0.3.0.tar.gz#sha256=7dc7854f0140d370e408b03eed00b9a8be51b382bd5ee60a10aea58706a2206b (from https://pypi.org/simple/mdreg/) (requires-python:>=3.6, <4), version: 0.3.0
2022-04-08T11:11:25,544   Skipping link: No binaries permitted for mdreg: https://files.pythonhosted.org/packages/6b/67/cd996be7b682acd1e126cc4e01f6f267fbfff5a7e5fca5c51e065c7b4497/mdreg-0.3.1-py3-none-any.whl#sha256=e3582f07ac52f4ad5b334091e8e595b32bcfb8c67c7e456920bb82eea4ba5ad4 (from https://pypi.org/simple/mdreg/) (requires-python:>=3.6, <4)
2022-04-08T11:11:25,545   Found link https://files.pythonhosted.org/packages/eb/8b/0358e3454beda70f4259a4d86932f6e072225039955f5a20d39144173ede/mdreg-0.3.1.tar.gz#sha256=8f5b490139cbe17e3c0bc07922cd8dbe529740485daf98ed0e594715236837e9 (from https://pypi.org/simple/mdreg/) (requires-python:>=3.6, <4), version: 0.3.1
2022-04-08T11:11:25,546 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdreg/
2022-04-08T11:11:25,547 Getting page https://www.piwheels.org/simple/mdreg/
2022-04-08T11:11:25,549 Found index url https://www.piwheels.org/simple
2022-04-08T11:11:25,771 Skipping link: not a file: https://www.piwheels.org/simple/mdreg/
2022-04-08T11:11:25,772 Skipping link: not a file: https://pypi.org/simple/mdreg/
2022-04-08T11:11:25,805 Given no hashes to check 1 links for project 'mdreg': discarding no candidates
2022-04-08T11:11:25,836 Collecting mdreg==0.3.1
2022-04-08T11:11:25,841   Created temporary directory: /tmp/pip-unpack-1k7hyyv9
2022-04-08T11:11:26,067   Downloading mdreg-0.3.1.tar.gz (21 kB)
2022-04-08T11:11:26,193   Added mdreg==0.3.1 from https://files.pythonhosted.org/packages/eb/8b/0358e3454beda70f4259a4d86932f6e072225039955f5a20d39144173ede/mdreg-0.3.1.tar.gz#sha256=8f5b490139cbe17e3c0bc07922cd8dbe529740485daf98ed0e594715236837e9 to build tracker '/tmp/pip-req-tracker-xtm8fgqm'
2022-04-08T11:11:26,195   Running setup.py (path:/tmp/pip-wheel-qrnv_8wt/mdreg_7450a7b9a1a0470c9b22182853ef0e83/setup.py) egg_info for package mdreg
2022-04-08T11:11:26,196   Created temporary directory: /tmp/pip-pip-egg-info-moq81xr8
2022-04-08T11:11:26,197   Preparing metadata (setup.py): started
2022-04-08T11:11:26,199   Running command python setup.py egg_info
2022-04-08T11:11:27,866   Traceback (most recent call last):
2022-04-08T11:11:27,868     File "<string>", line 36, in <module>
2022-04-08T11:11:27,868     File "<pip-setuptools-caller>", line 34, in <module>
2022-04-08T11:11:27,869     File "/tmp/pip-wheel-qrnv_8wt/mdreg_7450a7b9a1a0470c9b22182853ef0e83/setup.py", line 13, in <module>
2022-04-08T11:11:27,869       with open('requirements.txt', encoding='utf-8') as f:
2022-04-08T11:11:27,870   FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'
2022-04-08T11:11:27,870   # Description
2022-04-08T11:11:27,871   Python implementation of model-based image coregistration
2022-04-08T11:11:27,871   for quantitative medical imaging applications.

2022-04-08T11:11:27,872   The distribution comes with a number of common signal models and uses [ITK-Elastix](https://github.com/InsightSoftwareConsortium/ITKElastix) for deformable image registration.

2022-04-08T11:11:27,873   ## Installation
2022-04-08T11:11:27,874   Run `pip install mdreg`.

2022-04-08T11:11:27,875   ## Example data
2022-04-08T11:11:27,875   Example data in [DICOM format](https://shorturl.at/rwCUV) are provided for testing the setup.

2022-04-08T11:11:27,876   ## How to use
2022-04-08T11:11:27,877   Input data must be image arrays in numpy format, with dimensions `(x,y,z,t)` or `(x,y,t)`.
2022-04-08T11:11:27,877   To perform MDR on an image array `im` with default settings do:

2022-04-08T11:11:27,878   ```python
2022-04-08T11:11:27,878   from mdreg import MDReg

2022-04-08T11:11:27,879   mdr = MDReg()
2022-04-08T11:11:27,880   mdr.set_array(im)
2022-04-08T11:11:27,880   mdr.fit()
2022-04-08T11:11:27,880   ```

2022-04-08T11:11:27,881   When fitting is complete the motion-corrected data are in `mdr.coreg` in the same dimensions
2022-04-08T11:11:27,882   as the original `im`. The calculated deformation fields in format `(x,y,d,t)` or `(x,y,z,d,t)`
2022-04-08T11:11:27,882   can be found as `mdr.deformation`. The dimension `d` holds `x`, `y` components
2022-04-08T11:11:27,882   of the deformation field, and a third `z` component if the input array is 3D.

2022-04-08T11:11:27,883   The default settings will apply a linear signal model and coregistration
2022-04-08T11:11:27,884   as defined in the elastix parameter file `Bsplines.txt`.

2022-04-08T11:11:27,885   # Customization

2022-04-08T11:11:27,885   MDR can be configured to apply different signal models and elastix coregistration settings.
2022-04-08T11:11:27,886   A number of example models and alternative elastix parameter files are included
2022-04-08T11:11:27,886   in the distribution as templates.

2022-04-08T11:11:27,887   The following example fits a mono-exponential decay, uses a mask `im_mask` for co-registration and applies an elastix parameter file `par_file` optimized for a previous DTI-MRI study:

2022-04-08T11:11:27,888   ```python
2022-04-08T11:11:27,889   from mdreg import MDReg
2022-04-08T11:11:27,889   from mdreg.models import exponential_decay

2022-04-08T11:11:27,890   mdr = MDReg()
2022-04-08T11:11:27,890   mdr.set_array(im)
2022-04-08T11:11:27,891   mdr.set_mask(im_mask)
2022-04-08T11:11:27,891   mdr.signal_model = exponential_decay
2022-04-08T11:11:27,892   mdr.read_elastix(par_file)
2022-04-08T11:11:27,892   mdr.fit()
2022-04-08T11:11:27,892   ```

2022-04-08T11:11:27,893   `im_mask` must be a binary (0s and 1s) or boolean (Trues and Falses) image array in numpy format with the same dimensions as `im`.

2022-04-08T11:11:27,894   The signal model often depends on fixed constants and signal parameters
2022-04-08T11:11:27,894   such as sequence parameters in MRI, or patient-specific constants. These
2022-04-08T11:11:27,894   should all be grouped in a list and set before running the signal model.

2022-04-08T11:11:27,895   Equally elastix parameters can be fine tuned, either by importing a
2022-04-08T11:11:27,896   dedicated elastix file, or by modifying the settings.

2022-04-08T11:11:27,897   You may also choose if you wish to run the process in multiple cores (`parallel`) and to print the co-registration progress to the terminal plus a text file (`log`) or not.

2022-04-08T11:11:27,898   Then, a number of parameters are available to optimize MDR such as
2022-04-08T11:11:27,898   the precision (stopping criterion) and maximum number of iterations.

2022-04-08T11:11:27,899   Some examples:

2022-04-08T11:11:27,900   ```python
2022-04-08T11:11:27,900   from mdreg import MDReg
2022-04-08T11:11:27,901   from mdreg.models import exponential_decay

2022-04-08T11:11:27,902   t = [0.0, 1.25, 2.50, 3.75]     # time points for exponential in sec

2022-04-08T11:11:27,902   mdr = MDReg()
2022-04-08T11:11:27,903   mdr.set_array(im)
2022-04-08T11:11:27,903   mdr.signal_parameters = t
2022-04-08T11:11:27,904   mdr.signal_model = exponential_decay
2022-04-08T11:11:27,904   mdr.set_elastix(MaximumNumberOfIterations = 256)   # change defaults
2022-04-08T11:11:27,904   mdr.precision = 0.5         # default = 1
2022-04-08T11:11:27,905   mdr.max_iterations = 3      # default = 5
2022-04-08T11:11:27,905   mdr.parallel = False        # default = True
2022-04-08T11:11:27,906   mdr.log = True              # default = False
2022-04-08T11:11:27,906   mdr.fit()
2022-04-08T11:11:27,907   ```

2022-04-08T11:11:27,907   `mdreg` comes with a number of options to
2022-04-08T11:11:27,908   export results and diagnostics:

2022-04-08T11:11:27,909   ```python
2022-04-08T11:11:27,909   mdr.export_unregistered = True      # export parameters and fit without registration
2022-04-08T11:11:27,910   mdr.export_path = filepath          # default is a results folder in the current working directory
2022-04-08T11:11:27,910   mdr.export()                        # export results after calling fit.
2022-04-08T11:11:27,911   ```

2022-04-08T11:11:27,912   This export creates movies of original images, motion corrected images,
2022-04-08T11:11:27,912   modelfits, and maps of the fitted parameters.

2022-04-08T11:11:27,913   # Model fitting without motion correction

2022-04-08T11:11:27,914   `MDReg` also can be used to perform model fitting
2022-04-08T11:11:27,914   without correcting the motion. The following script
2022-04-08T11:11:27,915   fits a linearised exponential model to each pixel and exports data
2022-04-08T11:11:27,915   of model and fit:

2022-04-08T11:11:27,916   ```python
2022-04-08T11:11:27,916   from mdreg import MDReg
2022-04-08T11:11:27,917   from mdreg.models import exponential_decay

2022-04-08T11:11:27,918   mdr = MDReg()
2022-04-08T11:11:27,918   mdr.set_array(im)
2022-04-08T11:11:27,918   mdr.signal_model = linear_exponential_decay
2022-04-08T11:11:27,919   mdr.fit_signal()
2022-04-08T11:11:27,919   mdr.export_data()
2022-04-08T11:11:27,920   mdr.export_fit()
2022-04-08T11:11:27,920   ```

2022-04-08T11:11:27,921   # Defining new MDR models

2022-04-08T11:11:27,922   A model must be defined as a separate module or class with two required functions `main()` and `pars()`.

2022-04-08T11:11:27,922   `pars()` must return a list of strings specifying the names of the model parameters.
2022-04-08T11:11:27,923   `main(im, const)` performs the pixel based model fitting and has two required arguments.
2022-04-08T11:11:27,923   `im` is a numpy ndarray with dimensions `(x,y,z,t)`, `(x,y,t)` or `(x,t)`. `const` is a list
2022-04-08T11:11:27,924   of any constant model parameters.

2022-04-08T11:11:27,924   The function must return the fit to the model as an numpy ndarray with the same dimensions
2022-04-08T11:11:27,925   as `im`, and an ndarray `pars` with dimensions `(x,y,z,p)`, `(x,y,p)` or `(x,p)`. Here `p` enumerates
2022-04-08T11:11:27,925   the model parameters.

2022-04-08T11:11:27,926   ## Context

2022-04-08T11:11:27,926   `mdreg` was first developed for use in quantitative renal MRI in the iBEAt study,
2022-04-08T11:11:27,927   and validated against group-wise model-free registration
2022-04-08T11:11:27,927   (Tagkalakis F, et al. Model-based motion correction outperforms a model-free method in quantitative renal MRI. Abstract-1383, ISMRM 2021).

2022-04-08T11:11:27,928   ## Acknowledgement

2022-04-08T11:11:27,928   The iBEAt study is part of the BEAt-DKD project. The BEAt-DKD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 115974. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA with JDRF. For a full list of BEAt-DKD partners, see www.beat-dkd.eu.

2022-04-08T11:11:27,929   ## Authors

2022-04-08T11:11:27,929   Kanishka Sharma, Joao Almeida e Sousa, Steven Sourbron

2022-04-08T11:11:27,974   ERROR: [present-diagnostic] python setup.py egg_info exited with 1
2022-04-08T11:11:28,021   [bold magenta]full command[/]: [blue]/usr/bin/python3 -c '
2022-04-08T11:11:28,021   exec(compile('"'"''"'"''"'"'
2022-04-08T11:11:28,021   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2022-04-08T11:11:28,021   #
2022-04-08T11:11:28,021   # - It imports setuptools before invoking setup.py, to enable projects that directly
2022-04-08T11:11:28,021   #   import from `distutils.core` to work with newer packaging standards.
2022-04-08T11:11:28,021   # - It provides a clear error message when setuptools is not installed.
2022-04-08T11:11:28,021   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2022-04-08T11:11:28,021   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2022-04-08T11:11:28,021   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2022-04-08T11:11:28,021   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2022-04-08T11:11:28,021   import os, sys, tokenize
2022-04-08T11:11:28,021   
2022-04-08T11:11:28,021   try:
2022-04-08T11:11:28,021       import setuptools
2022-04-08T11:11:28,021   except ImportError as error:
2022-04-08T11:11:28,021       print(
2022-04-08T11:11:28,021           "ERROR: Can not execute `setup.py` since setuptools is not available in "
2022-04-08T11:11:28,021           "the build environment.",
2022-04-08T11:11:28,021           file=sys.stderr,
2022-04-08T11:11:28,021       )
2022-04-08T11:11:28,021       sys.exit(1)
2022-04-08T11:11:28,021   
2022-04-08T11:11:28,021   __file__ = %r
2022-04-08T11:11:28,021   sys.argv[0] = __file__
2022-04-08T11:11:28,021   
2022-04-08T11:11:28,021   if os.path.exists(__file__):
2022-04-08T11:11:28,021       filename = __file__
2022-04-08T11:11:28,021       with tokenize.open(__file__) as f:
2022-04-08T11:11:28,021           setup_py_code = f.read()
2022-04-08T11:11:28,021   else:
2022-04-08T11:11:28,021       filename = "<auto-generated setuptools caller>"
2022-04-08T11:11:28,021       setup_py_code = "from setuptools import setup; setup()"
2022-04-08T11:11:28,021   
2022-04-08T11:11:28,021   exec(compile(setup_py_code, filename, "exec"))
2022-04-08T11:11:28,021   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-qrnv_8wt/mdreg_7450a7b9a1a0470c9b22182853ef0e83/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-moq81xr8[/]
2022-04-08T11:11:28,022   [bold magenta]cwd[/]: /tmp/pip-wheel-qrnv_8wt/mdreg_7450a7b9a1a0470c9b22182853ef0e83/
2022-04-08T11:11:28,022   Preparing metadata (setup.py): finished with status 'error'
2022-04-08T11:11:28,025 ERROR: [present-diagnostic] metadata generation failed
2022-04-08T11:11:28,039 Exception information:
2022-04-08T11:11:28,039 Traceback (most recent call last):
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 68, in generate_metadata
2022-04-08T11:11:28,039     spinner=spinner,
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess
2022-04-08T11:11:28,039     raise error
2022-04-08T11:11:28,039 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1
2022-04-08T11:11:28,039 
2022-04-08T11:11:28,039 The above exception was the direct cause of the following exception:
2022-04-08T11:11:28,039 
2022-04-08T11:11:28,039 Traceback (most recent call last):
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 167, in exc_logging_wrapper
2022-04-08T11:11:28,039     status = run_func(*args)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2022-04-08T11:11:28,039     return func(self, options, args)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 145, in run
2022-04-08T11:11:28,039     requirement_set = resolver.resolve(reqs, check_supported_wheels=True)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 95, in resolve
2022-04-08T11:11:28,039     collected.requirements, max_rounds=try_to_avoid_resolution_too_deep
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 481, in resolve
2022-04-08T11:11:28,039     state = resolution.resolve(requirements, max_rounds=max_rounds)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 348, in resolve
2022-04-08T11:11:28,039     self._add_to_criteria(self.state.criteria, r, parent=None)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 172, in _add_to_criteria
2022-04-08T11:11:28,039     if not criterion.candidates:
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_vendor/resolvelib/structs.py", line 151, in __bool__
2022-04-08T11:11:28,039     return bool(self._sequence)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__
2022-04-08T11:11:28,039     return any(self)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in <genexpr>
2022-04-08T11:11:28,039     return (c for c in iterator if id(c) not in self._incompatible_ids)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
2022-04-08T11:11:28,039     candidate = func()
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 220, in _make_candidate_from_link
2022-04-08T11:11:28,039     version=version,
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 294, in __init__
2022-04-08T11:11:28,039     version=version,
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 158, in __init__
2022-04-08T11:11:28,039     self.dist = self._prepare()
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 227, in _prepare
2022-04-08T11:11:28,039     dist = self._prepare_distribution()
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 299, in _prepare_distribution
2022-04-08T11:11:28,039     return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 487, in prepare_linked_requirement
2022-04-08T11:11:28,039     return self._prepare_linked_requirement(req, parallel_builds)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 560, in _prepare_linked_requirement
2022-04-08T11:11:28,039     self.build_isolation,
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 58, in _get_prepared_distribution
2022-04-08T11:11:28,039     abstract_dist.prepare_distribution_metadata(finder, build_isolation)
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/distributions/sdist.py", line 47, in prepare_distribution_metadata
2022-04-08T11:11:28,039     self.req.prepare_metadata()
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 533, in prepare_metadata
2022-04-08T11:11:28,039     details=details,
2022-04-08T11:11:28,039   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata
2022-04-08T11:11:28,039     raise MetadataGenerationFailed(package_details=details) from error
2022-04-08T11:11:28,039 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed
2022-04-08T11:11:28,061 Removed mdreg==0.3.1 from https://files.pythonhosted.org/packages/eb/8b/0358e3454beda70f4259a4d86932f6e072225039955f5a20d39144173ede/mdreg-0.3.1.tar.gz#sha256=8f5b490139cbe17e3c0bc07922cd8dbe529740485daf98ed0e594715236837e9 from build tracker '/tmp/pip-req-tracker-xtm8fgqm'
2022-04-08T11:11:28,062 Removed build tracker: '/tmp/pip-req-tracker-xtm8fgqm'