diff --git a/docs/source/data.rst b/docs/source/data.rst index 9a667bdf..ca02da67 100644 --- a/docs/source/data.rst +++ b/docs/source/data.rst @@ -17,3 +17,36 @@ dataset (200 files, 725 MB). It was prepared with the following script: python scripts/prepare_mirflickr_subset.py \ --data ~/Documents/DiffuserCam/DiffuserCam_Mirflickr_Dataset + + +3D data +------- + +You can download example 3D PSF and raw data from the Waller lab +`here `__. +The PSF has to be converted from .mat to .npy in order to be usable : + +.. code:: bash + + python scripts/data/3d/mat_to_npy.py ~/path/to/example_psfs.mat + + +Once you have run a reconstruction, you may want to convert the +resulting .npy files in separate tiff images for each depth. +This can be done with the following script : + +.. code:: bash + + python scripts/data/3d/npy_to_tiff.py ~path/to/output.npy + + +You may also want to export it into a wavefront .obj file +for it to be displayed in 3D rendering softwares with the following +scrpit. It mostly exists to allow the user to preview it and is not +totally accurate as the problem of converting discrete pixels in a +"continuous" wavefront object is subject to interpreatation : + +.. code:: bash + + python scripts/data/3d/npy_to_obj.py ~/path/to/output.npy + \ No newline at end of file diff --git a/docs/source/simulation.rst b/docs/source/simulation.rst index 003354f6..89349040 100644 --- a/docs/source/simulation.rst +++ b/docs/source/simulation.rst @@ -15,3 +15,10 @@ library is used with the following simulation steps: #. **Quantize** according to the bit depth of the sensor. PyTorch support is available to speed up simulation on GPU, and to create Dataset and DataLoader objects for training and testing! + +Simulating 3D data +------------------ + +Check out `this other Medium post `__. + +The corresponding code will likely be added soon in waveprop. \ No newline at end of file diff --git a/lensless_docs/bin/Activate.ps1 b/lensless_docs/bin/Activate.ps1 new file mode 100644 index 00000000..2fb3852c --- /dev/null +++ b/lensless_docs/bin/Activate.ps1 @@ -0,0 +1,241 @@ +<# +.Synopsis +Activate a Python virtual environment for the current PowerShell session. + +.Description +Pushes the python executable for a virtual environment to the front of the +$Env:PATH environment variable and sets the prompt to signify that you are +in a Python virtual environment. Makes use of the command line switches as +well as the `pyvenv.cfg` file values present in the virtual environment. + +.Parameter VenvDir +Path to the directory that contains the virtual environment to activate. The +default value for this is the parent of the directory that the Activate.ps1 +script is located within. + +.Parameter Prompt +The prompt prefix to display when this virtual environment is activated. By +default, this prompt is the name of the virtual environment folder (VenvDir) +surrounded by parentheses and followed by a single space (ie. '(.venv) '). + +.Example +Activate.ps1 +Activates the Python virtual environment that contains the Activate.ps1 script. + +.Example +Activate.ps1 -Verbose +Activates the Python virtual environment that contains the Activate.ps1 script, +and shows extra information about the activation as it executes. + +.Example +Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv +Activates the Python virtual environment located in the specified location. + +.Example +Activate.ps1 -Prompt "MyPython" +Activates the Python virtual environment that contains the Activate.ps1 script, +and prefixes the current prompt with the specified string (surrounded in +parentheses) while the virtual environment is active. + +.Notes +On Windows, it may be required to enable this Activate.ps1 script by setting the +execution policy for the user. You can do this by issuing the following PowerShell +command: + +PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser + +For more information on Execution Policies: +https://go.microsoft.com/fwlink/?LinkID=135170 + +#> +Param( + [Parameter(Mandatory = $false)] + [String] + $VenvDir, + [Parameter(Mandatory = $false)] + [String] + $Prompt +) + +<# Function declarations --------------------------------------------------- #> + +<# +.Synopsis +Remove all shell session elements added by the Activate script, including the +addition of the virtual environment's Python executable from the beginning of +the PATH variable. + +.Parameter NonDestructive +If present, do not remove this function from the global namespace for the +session. + +#> +function global:deactivate ([switch]$NonDestructive) { + # Revert to original values + + # The prior prompt: + if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) { + Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt + Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT + } + + # The prior PYTHONHOME: + if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) { + Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME + Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME + } + + # The prior PATH: + if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) { + Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH + Remove-Item -Path Env:_OLD_VIRTUAL_PATH + } + + # Just remove the VIRTUAL_ENV altogether: + if (Test-Path -Path Env:VIRTUAL_ENV) { + Remove-Item -Path env:VIRTUAL_ENV + } + + # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether: + if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) { + Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force + } + + # Leave deactivate function in the global namespace if requested: + if (-not $NonDestructive) { + Remove-Item -Path function:deactivate + } +} + +<# +.Description +Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the +given folder, and returns them in a map. + +For each line in the pyvenv.cfg file, if that line can be parsed into exactly +two strings separated by `=` (with any amount of whitespace surrounding the =) +then it is considered a `key = value` line. The left hand string is the key, +the right hand is the value. + +If the value starts with a `'` or a `"` then the first and last character is +stripped from the value before being captured. + +.Parameter ConfigDir +Path to the directory that contains the `pyvenv.cfg` file. +#> +function Get-PyVenvConfig( + [String] + $ConfigDir +) { + Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg" + + # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue). + $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue + + # An empty map will be returned if no config file is found. + $pyvenvConfig = @{ } + + if ($pyvenvConfigPath) { + + Write-Verbose "File exists, parse `key = value` lines" + $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath + + $pyvenvConfigContent | ForEach-Object { + $keyval = $PSItem -split "\s*=\s*", 2 + if ($keyval[0] -and $keyval[1]) { + $val = $keyval[1] + + # Remove extraneous quotations around a string value. + if ("'""".Contains($val.Substring(0, 1))) { + $val = $val.Substring(1, $val.Length - 2) + } + + $pyvenvConfig[$keyval[0]] = $val + Write-Verbose "Adding Key: '$($keyval[0])'='$val'" + } + } + } + return $pyvenvConfig +} + + +<# Begin Activate script --------------------------------------------------- #> + +# Determine the containing directory of this script +$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition +$VenvExecDir = Get-Item -Path $VenvExecPath + +Write-Verbose "Activation script is located in path: '$VenvExecPath'" +Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)" +Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)" + +# Set values required in priority: CmdLine, ConfigFile, Default +# First, get the location of the virtual environment, it might not be +# VenvExecDir if specified on the command line. +if ($VenvDir) { + Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values" +} +else { + Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir." + $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/") + Write-Verbose "VenvDir=$VenvDir" +} + +# Next, read the `pyvenv.cfg` file to determine any required value such +# as `prompt`. +$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir + +# Next, set the prompt from the command line, or the config file, or +# just use the name of the virtual environment folder. +if ($Prompt) { + Write-Verbose "Prompt specified as argument, using '$Prompt'" +} +else { + Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value" + if ($pyvenvCfg -and $pyvenvCfg['prompt']) { + Write-Verbose " Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'" + $Prompt = $pyvenvCfg['prompt']; + } + else { + Write-Verbose " Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virutal environment)" + Write-Verbose " Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'" + $Prompt = Split-Path -Path $venvDir -Leaf + } +} + +Write-Verbose "Prompt = '$Prompt'" +Write-Verbose "VenvDir='$VenvDir'" + +# Deactivate any currently active virtual environment, but leave the +# deactivate function in place. +deactivate -nondestructive + +# Now set the environment variable VIRTUAL_ENV, used by many tools to determine +# that there is an activated venv. +$env:VIRTUAL_ENV = $VenvDir + +if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) { + + Write-Verbose "Setting prompt to '$Prompt'" + + # Set the prompt to include the env name + # Make sure _OLD_VIRTUAL_PROMPT is global + function global:_OLD_VIRTUAL_PROMPT { "" } + Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT + New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt + + function global:prompt { + Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) " + _OLD_VIRTUAL_PROMPT + } +} + +# Clear PYTHONHOME +if (Test-Path -Path Env:PYTHONHOME) { + Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME + Remove-Item -Path Env:PYTHONHOME +} + +# Add the venv to the PATH +Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH +$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH" diff --git a/lensless_docs/bin/activate b/lensless_docs/bin/activate new file mode 100644 index 00000000..a6003322 --- /dev/null +++ b/lensless_docs/bin/activate @@ -0,0 +1,76 @@ +# This file must be used with "source bin/activate" *from bash* +# you cannot run it directly + +deactivate () { + # reset old environment variables + if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then + PATH="${_OLD_VIRTUAL_PATH:-}" + export PATH + unset _OLD_VIRTUAL_PATH + fi + if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then + PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}" + export PYTHONHOME + unset _OLD_VIRTUAL_PYTHONHOME + fi + + # This should detect bash and zsh, which have a hash command that must + # be called to get it to forget past commands. Without forgetting + # past commands the $PATH changes we made may not be respected + if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r + fi + + if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then + PS1="${_OLD_VIRTUAL_PS1:-}" + export PS1 + unset _OLD_VIRTUAL_PS1 + fi + + unset VIRTUAL_ENV + if [ ! "${1:-}" = "nondestructive" ] ; then + # Self destruct! + unset -f deactivate + fi +} + +# unset irrelevant variables +deactivate nondestructive + +VIRTUAL_ENV="/home/julien-sahli/git/LenslessPiCam/lensless_docs" +export VIRTUAL_ENV + +_OLD_VIRTUAL_PATH="$PATH" +PATH="$VIRTUAL_ENV/bin:$PATH" +export PATH + +# unset PYTHONHOME if set +# this will fail if PYTHONHOME is set to the empty string (which is bad anyway) +# could use `if (set -u; : $PYTHONHOME) ;` in bash +if [ -n "${PYTHONHOME:-}" ] ; then + _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}" + unset PYTHONHOME +fi + +if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then + _OLD_VIRTUAL_PS1="${PS1:-}" + if [ "x(lensless_docs) " != x ] ; then + PS1="(lensless_docs) ${PS1:-}" + else + if [ "`basename \"$VIRTUAL_ENV\"`" = "__" ] ; then + # special case for Aspen magic directories + # see https://aspen.io/ + PS1="[`basename \`dirname \"$VIRTUAL_ENV\"\``] $PS1" + else + PS1="(`basename \"$VIRTUAL_ENV\"`)$PS1" + fi + fi + export PS1 +fi + +# This should detect bash and zsh, which have a hash command that must +# be called to get it to forget past commands. Without forgetting +# past commands the $PATH changes we made may not be respected +if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r +fi diff --git a/lensless_docs/bin/activate.csh b/lensless_docs/bin/activate.csh new file mode 100644 index 00000000..fbdf58d4 --- /dev/null +++ b/lensless_docs/bin/activate.csh @@ -0,0 +1,37 @@ +# This file must be used with "source bin/activate.csh" *from csh*. +# You cannot run it directly. +# Created by Davide Di Blasi . +# Ported to Python 3.3 venv by Andrew Svetlov + +alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate' + +# Unset irrelevant variables. +deactivate nondestructive + +setenv VIRTUAL_ENV "/home/julien-sahli/git/LenslessPiCam/lensless_docs" + +set _OLD_VIRTUAL_PATH="$PATH" +setenv PATH "$VIRTUAL_ENV/bin:$PATH" + + +set _OLD_VIRTUAL_PROMPT="$prompt" + +if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then + if ("lensless_docs" != "") then + set env_name = "lensless_docs" + else + if (`basename "VIRTUAL_ENV"` == "__") then + # special case for Aspen magic directories + # see https://aspen.io/ + set env_name = `basename \`dirname "$VIRTUAL_ENV"\`` + else + set env_name = `basename "$VIRTUAL_ENV"` + endif + endif + set prompt = "[$env_name] $prompt" + unset env_name +endif + +alias pydoc python -m pydoc + +rehash diff --git a/lensless_docs/bin/activate.fish b/lensless_docs/bin/activate.fish new file mode 100644 index 00000000..df751126 --- /dev/null +++ b/lensless_docs/bin/activate.fish @@ -0,0 +1,75 @@ +# This file must be used with ". bin/activate.fish" *from fish* (http://fishshell.org) +# you cannot run it directly + +function deactivate -d "Exit virtualenv and return to normal shell environment" + # reset old environment variables + if test -n "$_OLD_VIRTUAL_PATH" + set -gx PATH $_OLD_VIRTUAL_PATH + set -e _OLD_VIRTUAL_PATH + end + if test -n "$_OLD_VIRTUAL_PYTHONHOME" + set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME + set -e _OLD_VIRTUAL_PYTHONHOME + end + + if test -n "$_OLD_FISH_PROMPT_OVERRIDE" + functions -e fish_prompt + set -e _OLD_FISH_PROMPT_OVERRIDE + functions -c _old_fish_prompt fish_prompt + functions -e _old_fish_prompt + end + + set -e VIRTUAL_ENV + if test "$argv[1]" != "nondestructive" + # Self destruct! + functions -e deactivate + end +end + +# unset irrelevant variables +deactivate nondestructive + +set -gx VIRTUAL_ENV "/home/julien-sahli/git/LenslessPiCam/lensless_docs" + +set -gx _OLD_VIRTUAL_PATH $PATH +set -gx PATH "$VIRTUAL_ENV/bin" $PATH + +# unset PYTHONHOME if set +if set -q PYTHONHOME + set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME + set -e PYTHONHOME +end + +if test -z "$VIRTUAL_ENV_DISABLE_PROMPT" + # fish uses a function instead of an env var to generate the prompt. + + # save the current fish_prompt function as the function _old_fish_prompt + functions -c fish_prompt _old_fish_prompt + + # with the original prompt function renamed, we can override with our own. + function fish_prompt + # Save the return status of the last command + set -l old_status $status + + # Prompt override? + if test -n "(lensless_docs) " + printf "%s%s" "(lensless_docs) " (set_color normal) + else + # ...Otherwise, prepend env + set -l _checkbase (basename "$VIRTUAL_ENV") + if test $_checkbase = "__" + # special case for Aspen magic directories + # see https://aspen.io/ + printf "%s[%s]%s " (set_color -b blue white) (basename (dirname "$VIRTUAL_ENV")) (set_color normal) + else + printf "%s(%s)%s" (set_color -b blue white) (basename "$VIRTUAL_ENV") (set_color normal) + end + end + + # Restore the return status of the previous command. + echo "exit $old_status" | . + _old_fish_prompt + end + + set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV" +end diff --git a/lensless_docs/bin/easy_install b/lensless_docs/bin/easy_install new file mode 100755 index 00000000..ac7b3182 --- /dev/null +++ b/lensless_docs/bin/easy_install @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from setuptools.command.easy_install import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/easy_install-3.8 b/lensless_docs/bin/easy_install-3.8 new file mode 100755 index 00000000..ac7b3182 --- /dev/null +++ b/lensless_docs/bin/easy_install-3.8 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from setuptools.command.easy_install import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/f2py b/lensless_docs/bin/f2py new file mode 100755 index 00000000..56b83ad0 --- /dev/null +++ b/lensless_docs/bin/f2py @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from numpy.f2py.f2py2e import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/f2py3 b/lensless_docs/bin/f2py3 new file mode 100755 index 00000000..56b83ad0 --- /dev/null +++ b/lensless_docs/bin/f2py3 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from numpy.f2py.f2py2e import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/f2py3.8 b/lensless_docs/bin/f2py3.8 new file mode 100755 index 00000000..56b83ad0 --- /dev/null +++ b/lensless_docs/bin/f2py3.8 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from numpy.f2py.f2py2e import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/normalizer b/lensless_docs/bin/normalizer new file mode 100755 index 00000000..c2d659b3 --- /dev/null +++ b/lensless_docs/bin/normalizer @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from charset_normalizer.cli.normalizer import cli_detect +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(cli_detect()) diff --git a/lensless_docs/bin/pip b/lensless_docs/bin/pip new file mode 100755 index 00000000..6998704e --- /dev/null +++ b/lensless_docs/bin/pip @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/pip3 b/lensless_docs/bin/pip3 new file mode 100755 index 00000000..6998704e --- /dev/null +++ b/lensless_docs/bin/pip3 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/pip3.8 b/lensless_docs/bin/pip3.8 new file mode 100755 index 00000000..6998704e --- /dev/null +++ b/lensless_docs/bin/pip3.8 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/pybabel b/lensless_docs/bin/pybabel new file mode 100755 index 00000000..37165864 --- /dev/null +++ b/lensless_docs/bin/pybabel @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from babel.messages.frontend import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/pygmentize b/lensless_docs/bin/pygmentize new file mode 100755 index 00000000..f86a0c5e --- /dev/null +++ b/lensless_docs/bin/pygmentize @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pygments.cmdline import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/python b/lensless_docs/bin/python new file mode 120000 index 00000000..3ade0f6b --- /dev/null +++ b/lensless_docs/bin/python @@ -0,0 +1 @@ +/home/julien-sahli/git/LenslessPiCam/lensless_env/bin/python \ No newline at end of file diff --git a/lensless_docs/bin/python3 b/lensless_docs/bin/python3 new file mode 120000 index 00000000..d8654aa0 --- /dev/null +++ b/lensless_docs/bin/python3 @@ -0,0 +1 @@ +python \ No newline at end of file diff --git a/lensless_docs/bin/rst2html.py b/lensless_docs/bin/rst2html.py new file mode 100755 index 00000000..94ccaab8 --- /dev/null +++ b/lensless_docs/bin/rst2html.py @@ -0,0 +1,23 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2html.py 4564 2006-05-21 20:44:42Z wiemann $ +# Author: David Goodger +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing HTML. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description + + +description = ('Generates (X)HTML documents from standalone reStructuredText ' + 'sources. ' + default_description) + +publish_cmdline(writer_name='html', description=description) diff --git a/lensless_docs/bin/rst2html4.py b/lensless_docs/bin/rst2html4.py new file mode 100755 index 00000000..3b207cb7 --- /dev/null +++ b/lensless_docs/bin/rst2html4.py @@ -0,0 +1,26 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2html4.py 7994 2016-12-10 17:41:45Z milde $ +# Author: David Goodger +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing (X)HTML. + +The output conforms to XHTML 1.0 transitional +and almost to HTML 4.01 transitional (except for closing empty tags). +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description + + +description = ('Generates (X)HTML documents from standalone reStructuredText ' + 'sources. ' + default_description) + +publish_cmdline(writer_name='html4', description=description) diff --git a/lensless_docs/bin/rst2html5.py b/lensless_docs/bin/rst2html5.py new file mode 100755 index 00000000..a130decc --- /dev/null +++ b/lensless_docs/bin/rst2html5.py @@ -0,0 +1,35 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf8 -*- +# :Copyright: © 2015 Günter Milde. +# :License: Released under the terms of the `2-Clause BSD license`_, in short: +# +# Copying and distribution of this file, with or without modification, +# are permitted in any medium without royalty provided the copyright +# notice and this notice are preserved. +# This file is offered as-is, without any warranty. +# +# .. _2-Clause BSD license: http://www.spdx.org/licenses/BSD-2-Clause +# +# Revision: $Revision: 8410 $ +# Date: $Date: 2019-11-04 22:14:43 +0100 (Mo, 04. Nov 2019) $ + +""" +A minimal front end to the Docutils Publisher, producing HTML 5 documents. + +The output also conforms to XHTML 1.0 transitional +(except for the doctype declaration). +""" + +try: + import locale # module missing in Jython + locale.setlocale(locale.LC_ALL, '') +except locale.Error: + pass + +from docutils.core import publish_cmdline, default_description + +description = (u'Generates HTML 5 documents from standalone ' + u'reStructuredText sources ' + + default_description) + +publish_cmdline(writer_name='html5', description=description) diff --git a/lensless_docs/bin/rst2latex.py b/lensless_docs/bin/rst2latex.py new file mode 100755 index 00000000..54d69790 --- /dev/null +++ b/lensless_docs/bin/rst2latex.py @@ -0,0 +1,26 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2latex.py 5905 2009-04-16 12:04:49Z milde $ +# Author: David Goodger +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing LaTeX. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline + +description = ('Generates LaTeX documents from standalone reStructuredText ' + 'sources. ' + 'Reads from (default is stdin) and writes to ' + ' (default is stdout). See ' + ' for ' + 'the full reference.') + +publish_cmdline(writer_name='latex', description=description) diff --git a/lensless_docs/bin/rst2man.py b/lensless_docs/bin/rst2man.py new file mode 100755 index 00000000..60bbbc30 --- /dev/null +++ b/lensless_docs/bin/rst2man.py @@ -0,0 +1,26 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# Author: +# Contact: grubert@users.sf.net +# Copyright: This module has been placed in the public domain. + +""" +man.py +====== + +This module provides a simple command line interface that uses the +man page writer to output from ReStructuredText source. +""" + +import locale +try: + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description +from docutils.writers import manpage + +description = ("Generates plain unix manual documents. " + default_description) + +publish_cmdline(writer=manpage.Writer(), description=description) diff --git a/lensless_docs/bin/rst2odt.py b/lensless_docs/bin/rst2odt.py new file mode 100755 index 00000000..feb54f64 --- /dev/null +++ b/lensless_docs/bin/rst2odt.py @@ -0,0 +1,30 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2odt.py 5839 2009-01-07 19:09:28Z dkuhlman $ +# Author: Dave Kuhlman +# Copyright: This module has been placed in the public domain. + +""" +A front end to the Docutils Publisher, producing OpenOffice documents. +""" + +import sys +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline_to_binary, default_description +from docutils.writers.odf_odt import Writer, Reader + + +description = ('Generates OpenDocument/OpenOffice/ODF documents from ' + 'standalone reStructuredText sources. ' + default_description) + + +writer = Writer() +reader = Reader() +output = publish_cmdline_to_binary(reader=reader, writer=writer, + description=description) + diff --git a/lensless_docs/bin/rst2odt_prepstyles.py b/lensless_docs/bin/rst2odt_prepstyles.py new file mode 100755 index 00000000..15749a54 --- /dev/null +++ b/lensless_docs/bin/rst2odt_prepstyles.py @@ -0,0 +1,67 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2odt_prepstyles.py 8346 2019-08-26 12:11:32Z milde $ +# Author: Dave Kuhlman +# Copyright: This module has been placed in the public domain. + +""" +Fix a word-processor-generated styles.odt for odtwriter use: Drop page size +specifications from styles.xml in STYLE_FILE.odt. +""" + +# Author: Michael Schutte + +from __future__ import print_function + +from lxml import etree +import sys +import zipfile +from tempfile import mkstemp +import shutil +import os + +NAMESPACES = { + "style": "urn:oasis:names:tc:opendocument:xmlns:style:1.0", + "fo": "urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" +} + + +def prepstyle(filename): + + zin = zipfile.ZipFile(filename) + styles = zin.read("styles.xml") + + root = etree.fromstring(styles) + for el in root.xpath("//style:page-layout-properties", + namespaces=NAMESPACES): + for attr in el.attrib: + if attr.startswith("{%s}" % NAMESPACES["fo"]): + del el.attrib[attr] + + tempname = mkstemp() + zout = zipfile.ZipFile(os.fdopen(tempname[0], "w"), "w", + zipfile.ZIP_DEFLATED) + + for item in zin.infolist(): + if item.filename == "styles.xml": + zout.writestr(item, etree.tostring(root)) + else: + zout.writestr(item, zin.read(item.filename)) + + zout.close() + zin.close() + shutil.move(tempname[1], filename) + + +def main(): + args = sys.argv[1:] + if len(args) != 1: + print(__doc__, file=sys.stderr) + print("Usage: %s STYLE_FILE.odt\n" % sys.argv[0], file=sys.stderr) + sys.exit(1) + filename = args[0] + prepstyle(filename) + + +if __name__ == '__main__': + main() diff --git a/lensless_docs/bin/rst2pseudoxml.py b/lensless_docs/bin/rst2pseudoxml.py new file mode 100755 index 00000000..4c94dab9 --- /dev/null +++ b/lensless_docs/bin/rst2pseudoxml.py @@ -0,0 +1,23 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2pseudoxml.py 4564 2006-05-21 20:44:42Z wiemann $ +# Author: David Goodger +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing pseudo-XML. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description + + +description = ('Generates pseudo-XML from standalone reStructuredText ' + 'sources (for testing purposes). ' + default_description) + +publish_cmdline(description=description) diff --git a/lensless_docs/bin/rst2s5.py b/lensless_docs/bin/rst2s5.py new file mode 100755 index 00000000..0a7d98c7 --- /dev/null +++ b/lensless_docs/bin/rst2s5.py @@ -0,0 +1,24 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2s5.py 4564 2006-05-21 20:44:42Z wiemann $ +# Author: Chris Liechti +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing HTML slides using +the S5 template system. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description + + +description = ('Generates S5 (X)HTML slideshow documents from standalone ' + 'reStructuredText sources. ' + default_description) + +publish_cmdline(writer_name='s5', description=description) diff --git a/lensless_docs/bin/rst2xetex.py b/lensless_docs/bin/rst2xetex.py new file mode 100755 index 00000000..83a99727 --- /dev/null +++ b/lensless_docs/bin/rst2xetex.py @@ -0,0 +1,27 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2xetex.py 7847 2015-03-17 17:30:47Z milde $ +# Author: Guenter Milde +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing Lua/XeLaTeX code. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline + +description = ('Generates LaTeX documents from standalone reStructuredText ' + 'sources for compilation with the Unicode-aware TeX variants ' + 'XeLaTeX or LuaLaTeX. ' + 'Reads from (default is stdin) and writes to ' + ' (default is stdout). See ' + ' for ' + 'the full reference.') + +publish_cmdline(writer_name='xetex', description=description) diff --git a/lensless_docs/bin/rst2xml.py b/lensless_docs/bin/rst2xml.py new file mode 100755 index 00000000..3e252351 --- /dev/null +++ b/lensless_docs/bin/rst2xml.py @@ -0,0 +1,23 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rst2xml.py 4564 2006-05-21 20:44:42Z wiemann $ +# Author: David Goodger +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing Docutils XML. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description + + +description = ('Generates Docutils-native XML from standalone ' + 'reStructuredText sources. ' + default_description) + +publish_cmdline(writer_name='xml', description=description) diff --git a/lensless_docs/bin/rstpep2html.py b/lensless_docs/bin/rstpep2html.py new file mode 100755 index 00000000..696a2f77 --- /dev/null +++ b/lensless_docs/bin/rstpep2html.py @@ -0,0 +1,25 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python + +# $Id: rstpep2html.py 4564 2006-05-21 20:44:42Z wiemann $ +# Author: David Goodger +# Copyright: This module has been placed in the public domain. + +""" +A minimal front end to the Docutils Publisher, producing HTML from PEP +(Python Enhancement Proposal) documents. +""" + +try: + import locale + locale.setlocale(locale.LC_ALL, '') +except: + pass + +from docutils.core import publish_cmdline, default_description + + +description = ('Generates (X)HTML from reStructuredText-format PEP files. ' + + default_description) + +publish_cmdline(reader_name='pep', writer_name='pep_html', + description=description) diff --git a/lensless_docs/bin/sphinx-apidoc b/lensless_docs/bin/sphinx-apidoc new file mode 100755 index 00000000..b6eea31a --- /dev/null +++ b/lensless_docs/bin/sphinx-apidoc @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from sphinx.ext.apidoc import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/sphinx-autogen b/lensless_docs/bin/sphinx-autogen new file mode 100755 index 00000000..0c6ea225 --- /dev/null +++ b/lensless_docs/bin/sphinx-autogen @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from sphinx.ext.autosummary.generate import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/sphinx-build b/lensless_docs/bin/sphinx-build new file mode 100755 index 00000000..1e783b0f --- /dev/null +++ b/lensless_docs/bin/sphinx-build @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from sphinx.cmd.build import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/lensless_docs/bin/sphinx-quickstart b/lensless_docs/bin/sphinx-quickstart new file mode 100755 index 00000000..cd3eaced --- /dev/null +++ b/lensless_docs/bin/sphinx-quickstart @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/lensless_docs/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from sphinx.cmd.quickstart import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff 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b/python=3.9/bin/Activate.ps1 @@ -0,0 +1,241 @@ +<# +.Synopsis +Activate a Python virtual environment for the current PowerShell session. + +.Description +Pushes the python executable for a virtual environment to the front of the +$Env:PATH environment variable and sets the prompt to signify that you are +in a Python virtual environment. Makes use of the command line switches as +well as the `pyvenv.cfg` file values present in the virtual environment. + +.Parameter VenvDir +Path to the directory that contains the virtual environment to activate. The +default value for this is the parent of the directory that the Activate.ps1 +script is located within. + +.Parameter Prompt +The prompt prefix to display when this virtual environment is activated. By +default, this prompt is the name of the virtual environment folder (VenvDir) +surrounded by parentheses and followed by a single space (ie. '(.venv) '). + +.Example +Activate.ps1 +Activates the Python virtual environment that contains the Activate.ps1 script. + +.Example +Activate.ps1 -Verbose +Activates the Python virtual environment that contains the Activate.ps1 script, +and shows extra information about the activation as it executes. + +.Example +Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv +Activates the Python virtual environment located in the specified location. + +.Example +Activate.ps1 -Prompt "MyPython" +Activates the Python virtual environment that contains the Activate.ps1 script, +and prefixes the current prompt with the specified string (surrounded in +parentheses) while the virtual environment is active. + +.Notes +On Windows, it may be required to enable this Activate.ps1 script by setting the +execution policy for the user. You can do this by issuing the following PowerShell +command: + +PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser + +For more information on Execution Policies: +https://go.microsoft.com/fwlink/?LinkID=135170 + +#> +Param( + [Parameter(Mandatory = $false)] + [String] + $VenvDir, + [Parameter(Mandatory = $false)] + [String] + $Prompt +) + +<# Function declarations --------------------------------------------------- #> + +<# +.Synopsis +Remove all shell session elements added by the Activate script, including the +addition of the virtual environment's Python executable from the beginning of +the PATH variable. + +.Parameter NonDestructive +If present, do not remove this function from the global namespace for the +session. + +#> +function global:deactivate ([switch]$NonDestructive) { + # Revert to original values + + # The prior prompt: + if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) { + Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt + Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT + } + + # The prior PYTHONHOME: + if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) { + Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME + Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME + } + + # The prior PATH: + if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) { + Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH + Remove-Item -Path Env:_OLD_VIRTUAL_PATH + } + + # Just remove the VIRTUAL_ENV altogether: + if (Test-Path -Path Env:VIRTUAL_ENV) { + Remove-Item -Path env:VIRTUAL_ENV + } + + # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether: + if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) { + Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force + } + + # Leave deactivate function in the global namespace if requested: + if (-not $NonDestructive) { + Remove-Item -Path function:deactivate + } +} + +<# +.Description +Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the +given folder, and returns them in a map. + +For each line in the pyvenv.cfg file, if that line can be parsed into exactly +two strings separated by `=` (with any amount of whitespace surrounding the =) +then it is considered a `key = value` line. The left hand string is the key, +the right hand is the value. + +If the value starts with a `'` or a `"` then the first and last character is +stripped from the value before being captured. + +.Parameter ConfigDir +Path to the directory that contains the `pyvenv.cfg` file. +#> +function Get-PyVenvConfig( + [String] + $ConfigDir +) { + Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg" + + # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue). + $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue + + # An empty map will be returned if no config file is found. + $pyvenvConfig = @{ } + + if ($pyvenvConfigPath) { + + Write-Verbose "File exists, parse `key = value` lines" + $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath + + $pyvenvConfigContent | ForEach-Object { + $keyval = $PSItem -split "\s*=\s*", 2 + if ($keyval[0] -and $keyval[1]) { + $val = $keyval[1] + + # Remove extraneous quotations around a string value. + if ("'""".Contains($val.Substring(0, 1))) { + $val = $val.Substring(1, $val.Length - 2) + } + + $pyvenvConfig[$keyval[0]] = $val + Write-Verbose "Adding Key: '$($keyval[0])'='$val'" + } + } + } + return $pyvenvConfig +} + + +<# Begin Activate script --------------------------------------------------- #> + +# Determine the containing directory of this script +$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition +$VenvExecDir = Get-Item -Path $VenvExecPath + +Write-Verbose "Activation script is located in path: '$VenvExecPath'" +Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)" +Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)" + +# Set values required in priority: CmdLine, ConfigFile, Default +# First, get the location of the virtual environment, it might not be +# VenvExecDir if specified on the command line. +if ($VenvDir) { + Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values" +} +else { + Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir." + $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/") + Write-Verbose "VenvDir=$VenvDir" +} + +# Next, read the `pyvenv.cfg` file to determine any required value such +# as `prompt`. +$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir + +# Next, set the prompt from the command line, or the config file, or +# just use the name of the virtual environment folder. +if ($Prompt) { + Write-Verbose "Prompt specified as argument, using '$Prompt'" +} +else { + Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value" + if ($pyvenvCfg -and $pyvenvCfg['prompt']) { + Write-Verbose " Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'" + $Prompt = $pyvenvCfg['prompt']; + } + else { + Write-Verbose " Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virutal environment)" + Write-Verbose " Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'" + $Prompt = Split-Path -Path $venvDir -Leaf + } +} + +Write-Verbose "Prompt = '$Prompt'" +Write-Verbose "VenvDir='$VenvDir'" + +# Deactivate any currently active virtual environment, but leave the +# deactivate function in place. +deactivate -nondestructive + +# Now set the environment variable VIRTUAL_ENV, used by many tools to determine +# that there is an activated venv. +$env:VIRTUAL_ENV = $VenvDir + +if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) { + + Write-Verbose "Setting prompt to '$Prompt'" + + # Set the prompt to include the env name + # Make sure _OLD_VIRTUAL_PROMPT is global + function global:_OLD_VIRTUAL_PROMPT { "" } + Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT + New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt + + function global:prompt { + Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) " + _OLD_VIRTUAL_PROMPT + } +} + +# Clear PYTHONHOME +if (Test-Path -Path Env:PYTHONHOME) { + Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME + Remove-Item -Path Env:PYTHONHOME +} + +# Add the venv to the PATH +Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH +$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH" diff --git a/python=3.9/bin/activate b/python=3.9/bin/activate new file mode 100644 index 00000000..48dc6cd9 --- /dev/null +++ b/python=3.9/bin/activate @@ -0,0 +1,76 @@ +# This file must be used with "source bin/activate" *from bash* +# you cannot run it directly + +deactivate () { + # reset old environment variables + if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then + PATH="${_OLD_VIRTUAL_PATH:-}" + export PATH + unset _OLD_VIRTUAL_PATH + fi + if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then + PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}" + export PYTHONHOME + unset _OLD_VIRTUAL_PYTHONHOME + fi + + # This should detect bash and zsh, which have a hash command that must + # be called to get it to forget past commands. Without forgetting + # past commands the $PATH changes we made may not be respected + if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r + fi + + if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then + PS1="${_OLD_VIRTUAL_PS1:-}" + export PS1 + unset _OLD_VIRTUAL_PS1 + fi + + unset VIRTUAL_ENV + if [ ! "${1:-}" = "nondestructive" ] ; then + # Self destruct! + unset -f deactivate + fi +} + +# unset irrelevant variables +deactivate nondestructive + +VIRTUAL_ENV="/home/julien-sahli/git/LenslessPiCam/python=3.9" +export VIRTUAL_ENV + +_OLD_VIRTUAL_PATH="$PATH" +PATH="$VIRTUAL_ENV/bin:$PATH" +export PATH + +# unset PYTHONHOME if set +# this will fail if PYTHONHOME is set to the empty string (which is bad anyway) +# could use `if (set -u; : $PYTHONHOME) ;` in bash +if [ -n "${PYTHONHOME:-}" ] ; then + _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}" + unset PYTHONHOME +fi + +if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then + _OLD_VIRTUAL_PS1="${PS1:-}" + if [ "x(python=3.9) " != x ] ; then + PS1="(python=3.9) ${PS1:-}" + else + if [ "`basename \"$VIRTUAL_ENV\"`" = "__" ] ; then + # special case for Aspen magic directories + # see https://aspen.io/ + PS1="[`basename \`dirname \"$VIRTUAL_ENV\"\``] $PS1" + else + PS1="(`basename \"$VIRTUAL_ENV\"`)$PS1" + fi + fi + export PS1 +fi + +# This should detect bash and zsh, which have a hash command that must +# be called to get it to forget past commands. Without forgetting +# past commands the $PATH changes we made may not be respected +if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then + hash -r +fi diff --git a/python=3.9/bin/activate.csh b/python=3.9/bin/activate.csh new file mode 100644 index 00000000..63d4decf --- /dev/null +++ b/python=3.9/bin/activate.csh @@ -0,0 +1,37 @@ +# This file must be used with "source bin/activate.csh" *from csh*. +# You cannot run it directly. +# Created by Davide Di Blasi . +# Ported to Python 3.3 venv by Andrew Svetlov + +alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate' + +# Unset irrelevant variables. +deactivate nondestructive + +setenv VIRTUAL_ENV "/home/julien-sahli/git/LenslessPiCam/python=3.9" + +set _OLD_VIRTUAL_PATH="$PATH" +setenv PATH "$VIRTUAL_ENV/bin:$PATH" + + +set _OLD_VIRTUAL_PROMPT="$prompt" + +if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then + if ("python=3.9" != "") then + set env_name = "python=3.9" + else + if (`basename "VIRTUAL_ENV"` == "__") then + # special case for Aspen magic directories + # see https://aspen.io/ + set env_name = `basename \`dirname "$VIRTUAL_ENV"\`` + else + set env_name = `basename "$VIRTUAL_ENV"` + endif + endif + set prompt = "[$env_name] $prompt" + unset env_name +endif + +alias pydoc python -m pydoc + +rehash diff --git a/python=3.9/bin/activate.fish b/python=3.9/bin/activate.fish new file mode 100644 index 00000000..ce56bc72 --- /dev/null +++ b/python=3.9/bin/activate.fish @@ -0,0 +1,75 @@ +# This file must be used with ". bin/activate.fish" *from fish* (http://fishshell.org) +# you cannot run it directly + +function deactivate -d "Exit virtualenv and return to normal shell environment" + # reset old environment variables + if test -n "$_OLD_VIRTUAL_PATH" + set -gx PATH $_OLD_VIRTUAL_PATH + set -e _OLD_VIRTUAL_PATH + end + if test -n "$_OLD_VIRTUAL_PYTHONHOME" + set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME + set -e _OLD_VIRTUAL_PYTHONHOME + end + + if test -n "$_OLD_FISH_PROMPT_OVERRIDE" + functions -e fish_prompt + set -e _OLD_FISH_PROMPT_OVERRIDE + functions -c _old_fish_prompt fish_prompt + functions -e _old_fish_prompt + end + + set -e VIRTUAL_ENV + if test "$argv[1]" != "nondestructive" + # Self destruct! + functions -e deactivate + end +end + +# unset irrelevant variables +deactivate nondestructive + +set -gx VIRTUAL_ENV "/home/julien-sahli/git/LenslessPiCam/python=3.9" + +set -gx _OLD_VIRTUAL_PATH $PATH +set -gx PATH "$VIRTUAL_ENV/bin" $PATH + +# unset PYTHONHOME if set +if set -q PYTHONHOME + set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME + set -e PYTHONHOME +end + +if test -z "$VIRTUAL_ENV_DISABLE_PROMPT" + # fish uses a function instead of an env var to generate the prompt. + + # save the current fish_prompt function as the function _old_fish_prompt + functions -c fish_prompt _old_fish_prompt + + # with the original prompt function renamed, we can override with our own. + function fish_prompt + # Save the return status of the last command + set -l old_status $status + + # Prompt override? + if test -n "(python=3.9) " + printf "%s%s" "(python=3.9) " (set_color normal) + else + # ...Otherwise, prepend env + set -l _checkbase (basename "$VIRTUAL_ENV") + if test $_checkbase = "__" + # special case for Aspen magic directories + # see https://aspen.io/ + printf "%s[%s]%s " (set_color -b blue white) (basename (dirname "$VIRTUAL_ENV")) (set_color normal) + else + printf "%s(%s)%s" (set_color -b blue white) (basename "$VIRTUAL_ENV") (set_color normal) + end + end + + # Restore the return status of the previous command. + echo "exit $old_status" | . + _old_fish_prompt + end + + set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV" +end diff --git a/python=3.9/bin/easy_install b/python=3.9/bin/easy_install new file mode 100755 index 00000000..392a00c1 --- /dev/null +++ b/python=3.9/bin/easy_install @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/python=3.9/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from setuptools.command.easy_install import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/python=3.9/bin/easy_install-3.8 b/python=3.9/bin/easy_install-3.8 new file mode 100755 index 00000000..392a00c1 --- /dev/null +++ b/python=3.9/bin/easy_install-3.8 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/python=3.9/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from setuptools.command.easy_install import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/python=3.9/bin/pip b/python=3.9/bin/pip new file mode 100755 index 00000000..2b7ee0cd --- /dev/null +++ b/python=3.9/bin/pip @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/python=3.9/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/python=3.9/bin/pip3 b/python=3.9/bin/pip3 new file mode 100755 index 00000000..2b7ee0cd --- /dev/null +++ b/python=3.9/bin/pip3 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/python=3.9/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/python=3.9/bin/pip3.8 b/python=3.9/bin/pip3.8 new file mode 100755 index 00000000..2b7ee0cd --- /dev/null +++ b/python=3.9/bin/pip3.8 @@ -0,0 +1,8 @@ +#!/home/julien-sahli/git/LenslessPiCam/python=3.9/bin/python +# -*- coding: utf-8 -*- +import re +import sys +from pip._internal.cli.main import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) diff --git a/python=3.9/bin/python b/python=3.9/bin/python new file mode 120000 index 00000000..3ade0f6b --- /dev/null +++ b/python=3.9/bin/python @@ -0,0 +1 @@ +/home/julien-sahli/git/LenslessPiCam/lensless_env/bin/python \ No newline at end of file diff --git a/python=3.9/bin/python3 b/python=3.9/bin/python3 new file mode 120000 index 00000000..d8654aa0 --- /dev/null +++ b/python=3.9/bin/python3 @@ -0,0 +1 @@ +python \ No newline at end of file diff --git a/python=3.9/lib64 b/python=3.9/lib64 new file mode 120000 index 00000000..7951405f --- /dev/null +++ b/python=3.9/lib64 @@ -0,0 +1 @@ +lib \ No newline at end of file diff --git a/python=3.9/pyvenv.cfg b/python=3.9/pyvenv.cfg new file mode 100644 index 00000000..c9da8eed --- /dev/null +++ b/python=3.9/pyvenv.cfg @@ -0,0 +1,3 @@ +home = /home/julien-sahli/git/LenslessPiCam/lensless_env/bin +include-system-site-packages = false +version = 3.8.10 diff --git 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https://creativecommons.org/licenses/by/4.0/ - Link to the original work : https://www.saifkhichi.com/blog/blender-depth-map-surface-normals - -Instructions : - - Load or create any scene of your choice in blender (https://docs.blender.org/) - - Lots of scenes can be downloaded freely from websites such as https://www.blendswap.com/ - - You may want to set the background color of the scene to black ; otherwise, it will be - considered by the simulator as a physical plane which will be placed at the maximum depth - of the scene. To do so, the "Layout" tab, search the "World" menu on the right and, in the - "Surface" sub-menu, change the "Color" field to black. - If you forgot this step, you can still manually edit the exported image later to the image - editor of your choice in order to change the background pixels to black. - - - In the "Layout" tab, search the "View Layer Properties" menu on the right and mark the "Combined" and "Z" boxes - - - In the "Compositing" tab, add the following nodes : - - Tick "Use Nodes" to create two nodes : "Render Layer" and "Composite" - - Select "Add" -> "Output" -> "Viewer" to create a new node of the same name. - - Select "Add" -> "Vector" -> "Normalize" to create a new node of the same name. - - - Still in the "Compositing" tab, connect the nodes in the following way : - - Render Layer's field "Image" should already be connected to Composite's field Image. If not, connect it now. - - Connect Render Layer's field "Depth" to Normalize's input, which is the "Value" field at the bottom left. - - Connect Normalize's output, which is the "Value" field at the top right, to Viewer's field "Image" - - In Composite node, "Use Alpha" should already be ticked. If not, tick it now. - - In Viewer node, "Use Alpha" should already be ticked. If not, tick it now. - - - Still in the "Compositing" tab, in the Render Layer node, click on the Render button on bottom right - - - In the "Scripting" tab, go in the Text Editor field. It should be in the middle by default ; if not the case, open it - with the shortcut Shift+F11. Open the current field in it. Set the output path to your liking, then run the script. - - - Your data should now be properly exported at the specified path ! - -""" - -output_path = "/your/custom/path/" - -bpy.context.scene.render.filepath = output_path + "scene.png" -bpy.ops.render.render(False, animation=False, write_still=True) - -data = bpy.data.images['Viewer Node'] -w, h = data.size -depths = np.fliplr(np.rot90(np.reshape(np.array(data.pixels[:], dtype=np.float32), (h, w, 4))[:,:,0], k=2)) - -np.save(output_path + "scene-normals.npy", depths) diff --git a/scripts/conversion/mat_to_npy.py b/scripts/data/3d/mat_to_npy.py similarity index 100% rename from scripts/conversion/mat_to_npy.py rename to scripts/data/3d/mat_to_npy.py diff --git a/scripts/conversion/npy_to_obj.py b/scripts/data/3d/npy_to_obj.py similarity index 100% rename from scripts/conversion/npy_to_obj.py rename to scripts/data/3d/npy_to_obj.py diff --git a/scripts/conversion/npy_to_tiff.py b/scripts/data/3d/npy_to_tiff.py similarity index 91% rename from scripts/conversion/npy_to_tiff.py rename to scripts/data/3d/npy_to_tiff.py index 36654fc0..38c41a85 100644 --- a/scripts/conversion/npy_to_tiff.py +++ b/scripts/data/3d/npy_to_tiff.py @@ -1,5 +1,4 @@ -# This script is used to export the .mat paf from https://github.com/Waller-Lab/DiffuserCam/tree/master/example_data -# The output consists of the usable .npy file as well as tiff images for user visualisation +# This script is used to export each depth of a .npy 3D reconstruction into single tiff files for visualisation. import os import sys diff --git a/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/config.yaml b/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/config.yaml new file mode 100644 index 00000000..4238fa42 --- /dev/null +++ b/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/config.yaml @@ -0,0 +1,34 @@ +input: + psf: data/psf/tape_rgb.png + data: data/raw_data/thumbs_up_rgb.png + dtype: float32 +torch: false +torch_device: cpu +preprocess: + downsample: 4 + shape: null + flip: false + bayer: false + blue_gain: null + red_gain: null + single_psf: false + gray: false +display: + disp: 50 + plot: true + gamma: null +save: true +gradient_descent: + n_iter: 300 + method: fista + nesterov: + p: 0 + mu: 0.9 + fista: + tk: 1 +admm: + n_iter: 5 + mu1: 1.0e-06 + mu2: 1.0e-05 + mu3: 4.0e-05 + tau: 0.0001 diff --git a/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/hydra.yaml b/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/hydra.yaml new file mode 100644 index 00000000..47243e6f --- /dev/null +++ b/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/hydra.yaml @@ -0,0 +1,154 @@ +hydra: + run: + dir: outputs/${now:%Y-%m-%d}/${now:%H-%M-%S} + sweep: + dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S} + subdir: ${hydra.job.num} + launcher: + _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher + sweeper: + _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper + max_batch_size: null + params: null + help: + app_name: ${hydra.job.name} + header: '${hydra.help.app_name} is powered by Hydra. + + ' + footer: 'Powered by Hydra (https://hydra.cc) + + Use --hydra-help to view Hydra specific help + + ' + template: '${hydra.help.header} + + == Configuration groups == + + Compose your configuration from those groups (group=option) + + + $APP_CONFIG_GROUPS + + + == Config == + + Override anything in the config (foo.bar=value) + + + $CONFIG + + + ${hydra.help.footer} + + ' + hydra_help: + template: 'Hydra (${hydra.runtime.version}) + + See https://hydra.cc for more info. + + + == Flags == + + $FLAGS_HELP + + + == Configuration groups == + + Compose your configuration from those groups (For example, append hydra/job_logging=disabled + to command line) + + + $HYDRA_CONFIG_GROUPS + + + Use ''--cfg hydra'' to Show the Hydra config. + + ' + hydra_help: ??? + hydra_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][HYDRA] %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + root: + level: INFO + handlers: + - console + loggers: + logging_example: + level: DEBUG + disable_existing_loggers: false + job_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + file: + class: logging.FileHandler + formatter: simple + filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log + root: + level: INFO + handlers: + - console + - file + disable_existing_loggers: false + env: {} + mode: RUN + searchpath: [] + callbacks: {} + output_subdir: .hydra + overrides: + hydra: + - hydra.mode=RUN + task: [] + job: + name: gradient_descent + chdir: true + override_dirname: '' + id: ??? + num: ??? + config_name: defaults_recon + env_set: {} + env_copy: [] + config: + override_dirname: + kv_sep: '=' + item_sep: ',' + exclude_keys: [] + runtime: + version: 1.3.2 + version_base: '1.3' + cwd: /home/julien-sahli/git/LenslessPiCam/scripts/recon + config_sources: + - path: hydra.conf + schema: pkg + provider: hydra + - path: /home/julien-sahli/git/LenslessPiCam/configs + schema: file + provider: main + - path: '' + schema: structured + provider: schema + output_dir: /home/julien-sahli/git/LenslessPiCam/scripts/recon/outputs/2023-04-06/11-19-22 + choices: + hydra/env: default + hydra/callbacks: null + hydra/job_logging: default + hydra/hydra_logging: default + hydra/hydra_help: default + hydra/help: default + hydra/sweeper: basic + hydra/launcher: basic + hydra/output: default + verbose: false diff --git a/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/overrides.yaml b/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/overrides.yaml new file mode 100644 index 00000000..fe51488c --- /dev/null +++ b/scripts/recon/outputs/2023-04-06/11-19-22/.hydra/overrides.yaml @@ -0,0 +1 @@ +[] diff --git a/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/config.yaml b/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/config.yaml new file mode 100644 index 00000000..4238fa42 --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/config.yaml @@ -0,0 +1,34 @@ +input: + psf: data/psf/tape_rgb.png + data: data/raw_data/thumbs_up_rgb.png + dtype: float32 +torch: false +torch_device: cpu +preprocess: + downsample: 4 + shape: null + flip: false + bayer: false + blue_gain: null + red_gain: null + single_psf: false + gray: false +display: + disp: 50 + plot: true + gamma: null +save: true +gradient_descent: + n_iter: 300 + method: fista + nesterov: + p: 0 + mu: 0.9 + fista: + tk: 1 +admm: + n_iter: 5 + mu1: 1.0e-06 + mu2: 1.0e-05 + mu3: 4.0e-05 + tau: 0.0001 diff --git a/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/hydra.yaml b/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/hydra.yaml new file mode 100644 index 00000000..a03edf45 --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/hydra.yaml @@ -0,0 +1,154 @@ +hydra: + run: + dir: outputs/${now:%Y-%m-%d}/${now:%H-%M-%S} + sweep: + dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S} + subdir: ${hydra.job.num} + launcher: + _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher + sweeper: + _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper + max_batch_size: null + params: null + help: + app_name: ${hydra.job.name} + header: '${hydra.help.app_name} is powered by Hydra. + + ' + footer: 'Powered by Hydra (https://hydra.cc) + + Use --hydra-help to view Hydra specific help + + ' + template: '${hydra.help.header} + + == Configuration groups == + + Compose your configuration from those groups (group=option) + + + $APP_CONFIG_GROUPS + + + == Config == + + Override anything in the config (foo.bar=value) + + + $CONFIG + + + ${hydra.help.footer} + + ' + hydra_help: + template: 'Hydra (${hydra.runtime.version}) + + See https://hydra.cc for more info. + + + == Flags == + + $FLAGS_HELP + + + == Configuration groups == + + Compose your configuration from those groups (For example, append hydra/job_logging=disabled + to command line) + + + $HYDRA_CONFIG_GROUPS + + + Use ''--cfg hydra'' to Show the Hydra config. + + ' + hydra_help: ??? + hydra_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][HYDRA] %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + root: + level: INFO + handlers: + - console + loggers: + logging_example: + level: DEBUG + disable_existing_loggers: false + job_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + file: + class: logging.FileHandler + formatter: simple + filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log + root: + level: INFO + handlers: + - console + - file + disable_existing_loggers: false + env: {} + mode: RUN + searchpath: [] + callbacks: {} + output_subdir: .hydra + overrides: + hydra: + - hydra.mode=RUN + task: [] + job: + name: gradient_descent + chdir: true + override_dirname: '' + id: ??? + num: ??? + config_name: defaults_recon + env_set: {} + env_copy: [] + config: + override_dirname: + kv_sep: '=' + item_sep: ',' + exclude_keys: [] + runtime: + version: 1.3.2 + version_base: '1.3' + cwd: /home/julien-sahli/git/LenslessPiCam/scripts/recon + config_sources: + - path: hydra.conf + schema: pkg + provider: hydra + - path: /home/julien-sahli/git/LenslessPiCam/configs + schema: file + provider: main + - path: '' + schema: structured + provider: schema + output_dir: /home/julien-sahli/git/LenslessPiCam/scripts/recon/outputs/2023-04-18/13-59-33 + choices: + hydra/env: default + hydra/callbacks: null + hydra/job_logging: default + hydra/hydra_logging: default + hydra/hydra_help: default + hydra/help: default + hydra/sweeper: basic + hydra/launcher: basic + hydra/output: default + verbose: false diff --git a/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/overrides.yaml b/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/overrides.yaml new file mode 100644 index 00000000..fe51488c --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/13-59-33/.hydra/overrides.yaml @@ -0,0 +1 @@ +[] diff --git a/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/config.yaml b/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/config.yaml new file mode 100644 index 00000000..4238fa42 --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/config.yaml @@ -0,0 +1,34 @@ +input: + psf: data/psf/tape_rgb.png + data: data/raw_data/thumbs_up_rgb.png + dtype: float32 +torch: false +torch_device: cpu +preprocess: + downsample: 4 + shape: null + flip: false + bayer: false + blue_gain: null + red_gain: null + single_psf: false + gray: false +display: + disp: 50 + plot: true + gamma: null +save: true +gradient_descent: + n_iter: 300 + method: fista + nesterov: + p: 0 + mu: 0.9 + fista: + tk: 1 +admm: + n_iter: 5 + mu1: 1.0e-06 + mu2: 1.0e-05 + mu3: 4.0e-05 + tau: 0.0001 diff --git a/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/hydra.yaml b/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/hydra.yaml new file mode 100644 index 00000000..0ae30eda --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/hydra.yaml @@ -0,0 +1,154 @@ +hydra: + run: + dir: outputs/${now:%Y-%m-%d}/${now:%H-%M-%S} + sweep: + dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S} + subdir: ${hydra.job.num} + launcher: + _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher + sweeper: + _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper + max_batch_size: null + params: null + help: + app_name: ${hydra.job.name} + header: '${hydra.help.app_name} is powered by Hydra. + + ' + footer: 'Powered by Hydra (https://hydra.cc) + + Use --hydra-help to view Hydra specific help + + ' + template: '${hydra.help.header} + + == Configuration groups == + + Compose your configuration from those groups (group=option) + + + $APP_CONFIG_GROUPS + + + == Config == + + Override anything in the config (foo.bar=value) + + + $CONFIG + + + ${hydra.help.footer} + + ' + hydra_help: + template: 'Hydra (${hydra.runtime.version}) + + See https://hydra.cc for more info. + + + == Flags == + + $FLAGS_HELP + + + == Configuration groups == + + Compose your configuration from those groups (For example, append hydra/job_logging=disabled + to command line) + + + $HYDRA_CONFIG_GROUPS + + + Use ''--cfg hydra'' to Show the Hydra config. + + ' + hydra_help: ??? + hydra_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][HYDRA] %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + root: + level: INFO + handlers: + - console + loggers: + logging_example: + level: DEBUG + disable_existing_loggers: false + job_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + file: + class: logging.FileHandler + formatter: simple + filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log + root: + level: INFO + handlers: + - console + - file + disable_existing_loggers: false + env: {} + mode: RUN + searchpath: [] + callbacks: {} + output_subdir: .hydra + overrides: + hydra: + - hydra.mode=RUN + task: [] + job: + name: gradient_descent + chdir: true + override_dirname: '' + id: ??? + num: ??? + config_name: defaults_recon + env_set: {} + env_copy: [] + config: + override_dirname: + kv_sep: '=' + item_sep: ',' + exclude_keys: [] + runtime: + version: 1.3.2 + version_base: '1.3' + cwd: /home/julien-sahli/git/LenslessPiCam/scripts/recon + config_sources: + - path: hydra.conf + schema: pkg + provider: hydra + - path: /home/julien-sahli/git/LenslessPiCam/configs + schema: file + provider: main + - path: '' + schema: structured + provider: schema + output_dir: /home/julien-sahli/git/LenslessPiCam/scripts/recon/outputs/2023-04-18/14-18-16 + choices: + hydra/env: default + hydra/callbacks: null + hydra/job_logging: default + hydra/hydra_logging: default + hydra/hydra_help: default + hydra/help: default + hydra/sweeper: basic + hydra/launcher: basic + hydra/output: default + verbose: false diff --git a/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/overrides.yaml b/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/overrides.yaml new file mode 100644 index 00000000..fe51488c --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/14-18-16/.hydra/overrides.yaml @@ -0,0 +1 @@ +[] diff --git a/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/config.yaml b/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/config.yaml new file mode 100644 index 00000000..4238fa42 --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/config.yaml @@ -0,0 +1,34 @@ +input: + psf: data/psf/tape_rgb.png + data: data/raw_data/thumbs_up_rgb.png + dtype: float32 +torch: false +torch_device: cpu +preprocess: + downsample: 4 + shape: null + flip: false + bayer: false + blue_gain: null + red_gain: null + single_psf: false + gray: false +display: + disp: 50 + plot: true + gamma: null +save: true +gradient_descent: + n_iter: 300 + method: fista + nesterov: + p: 0 + mu: 0.9 + fista: + tk: 1 +admm: + n_iter: 5 + mu1: 1.0e-06 + mu2: 1.0e-05 + mu3: 4.0e-05 + tau: 0.0001 diff --git a/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/hydra.yaml b/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/hydra.yaml new file mode 100644 index 00000000..a2245964 --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/hydra.yaml @@ -0,0 +1,154 @@ +hydra: + run: + dir: outputs/${now:%Y-%m-%d}/${now:%H-%M-%S} + sweep: + dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S} + subdir: ${hydra.job.num} + launcher: + _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher + sweeper: + _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper + max_batch_size: null + params: null + help: + app_name: ${hydra.job.name} + header: '${hydra.help.app_name} is powered by Hydra. + + ' + footer: 'Powered by Hydra (https://hydra.cc) + + Use --hydra-help to view Hydra specific help + + ' + template: '${hydra.help.header} + + == Configuration groups == + + Compose your configuration from those groups (group=option) + + + $APP_CONFIG_GROUPS + + + == Config == + + Override anything in the config (foo.bar=value) + + + $CONFIG + + + ${hydra.help.footer} + + ' + hydra_help: + template: 'Hydra (${hydra.runtime.version}) + + See https://hydra.cc for more info. + + + == Flags == + + $FLAGS_HELP + + + == Configuration groups == + + Compose your configuration from those groups (For example, append hydra/job_logging=disabled + to command line) + + + $HYDRA_CONFIG_GROUPS + + + Use ''--cfg hydra'' to Show the Hydra config. + + ' + hydra_help: ??? + hydra_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][HYDRA] %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + root: + level: INFO + handlers: + - console + loggers: + logging_example: + level: DEBUG + disable_existing_loggers: false + job_logging: + version: 1 + formatters: + simple: + format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s' + handlers: + console: + class: logging.StreamHandler + formatter: simple + stream: ext://sys.stdout + file: + class: logging.FileHandler + formatter: simple + filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log + root: + level: INFO + handlers: + - console + - file + disable_existing_loggers: false + env: {} + mode: RUN + searchpath: [] + callbacks: {} + output_subdir: .hydra + overrides: + hydra: + - hydra.mode=RUN + task: [] + job: + name: gradient_descent + chdir: true + override_dirname: '' + id: ??? + num: ??? + config_name: defaults_recon + env_set: {} + env_copy: [] + config: + override_dirname: + kv_sep: '=' + item_sep: ',' + exclude_keys: [] + runtime: + version: 1.3.2 + version_base: '1.3' + cwd: /home/julien-sahli/git/LenslessPiCam/scripts/recon + config_sources: + - path: hydra.conf + schema: pkg + provider: hydra + - path: /home/julien-sahli/git/LenslessPiCam/configs + schema: file + provider: main + - path: '' + schema: structured + provider: schema + output_dir: /home/julien-sahli/git/LenslessPiCam/scripts/recon/outputs/2023-04-18/14-18-40 + choices: + hydra/env: default + hydra/callbacks: null + hydra/job_logging: default + hydra/hydra_logging: default + hydra/hydra_help: default + hydra/help: default + hydra/sweeper: basic + hydra/launcher: basic + hydra/output: default + verbose: false diff --git a/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/overrides.yaml b/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/overrides.yaml new file mode 100644 index 00000000..fe51488c --- /dev/null +++ b/scripts/recon/outputs/2023-04-18/14-18-40/.hydra/overrides.yaml @@ -0,0 +1 @@ +[]