STPSF

https://stpsf.readthedocs.io/en/latest/
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STPSF is a Python package that simulates point spread functions (PSFs) for NASA's James Webb Space...
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### Setup simulation to match file

Source: https://stpsf.readthedocs.io/en/latest/jwst_matching_psfs_to_data.html

Execute the setup function to configure the instrument object and load the closest-in-time wavefront sensing visit data.

```python
inst = stpsf.setup_sim_to_match_file(filename)
```

--------------------------------

### STPSF simulation setup output

Source: https://stpsf.readthedocs.io/en/latest/jwst_psf_subtraction.html

Example console output showing the MAST OPD query and instrument configuration details.

```text
Setting up sim to match jw02725-o484_t097_nircam_clear-f356w-nrcalong_wfscmb-04.fits
iterating query, tdelta=3.0

MAST OPD query around UTC: 2022-11-29T17:26:06.893
                        MJD: 59912.72646866898

OPD immediately preceding the given datetime:
        URI:     mast:JWST/product/R2022112903-NRCA3_FP1-1.fits
        Date (MJD):      59912.7265
        Delta time:      -0.0000 days

OPD immediately following the given datetime:
        URI:     mast:JWST/product/R2022120203-NRCA3_FP1-1.fits
        Date (MJD):      59915.1683
        Delta time:      2.4418 days
User requested choosing OPD time closest in time to 2022-11-29T17:26:06.893, which is R2022112903-NRCA3_FP1-1.fits, delta time -0.000 days
Importing and format-converting OPD from /Users/mperrin/software/stpsf-data/MAST_JWST_WSS_OPDs/R2022112903-NRCA3_FP1-1.fits
Backing out SI WFE and OTE field dependence at the WF sensing field point

Configured simulation instrument for:
    Instrument: NIRCam
    Filter: F356W
    Detector: NRCA5
    Apername: NRCA5_FULL
    Det. Pos.: (1024, 1024)
    Image plane mask: None
    Pupil plane mask: None
```

--------------------------------

### WebbPSF logging configuration output

Source: https://stpsf.readthedocs.io/en/latest/field_dependence/multifield_documentation.html

Example output showing the logging configuration for WebbPSF.

```text
WebbPSF log messages of level ERROR and above will be shown.
WebbPSF log outputs will be directed to the screen.
```

--------------------------------

### Instrument Initialization and Property Setup

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/stpsf_core.html

Initializes core instrument attributes including filters, masks, and detector configurations.

```python
        self.pupil_radius = None  # Set in subclass for JWST or Roman

        self.options = {}  # dict for storing other arbitrary options.

        # filter_list   available filter names in order by wavelength for public api
        # _filters      a dict of named tuples with name, filename, & default_nlambda
        #               with the filter name as the key
        self.filter_list, self._filters = self._get_filters()

        # choose a default filter, in case the user doesn't specify one
        self.filter = self.filter_list[0]

        self._rotation = None

        self._image_mask = None
        self.image_mask_list = []
        'List of available image_masks'

        self._pupil_mask = None
        self.pupil_mask_list = []
        'List of available pupil_masks'

        self.pixelscale = pixelscale
        'Detector pixel scale, in arcsec/pixel'
        self._spectra_cache = {}  # for caching synphot results.

        # n.b.STInstrument subclasses must set these
        self._detectors = {}
        self._detector = None
        self._detector_npixels = 2048
```

--------------------------------

### Setup STPSF environment

Source: https://stpsf.readthedocs.io/en/latest/_sources/field_dependence/multifield_documentation.ipynb.txt

Initializes the environment for STPSF by configuring matplotlib and importing necessary modules.

```python
%matplotlib inline
matplotlib.rcParams['image.origin'] = 'lower'
import stpsf
import astropy.units as u
stpsf.setup_logging()
```

--------------------------------

### setup_logging

Source: https://stpsf.readthedocs.io/en/latest/api_reference.html

Allows selection of logging detail and output locations (screen and/or file).

```APIDOC
## setup_logging

### Description
Allows selection of logging detail and output locations (screen and/or file).

### Method
Function

### Signature
`setup_logging([level, filename])`

### Parameters
- `level` (optional) - Logging level.
- `filename` (optional) - Output filename for log file.

### Returns
Configures logging settings.
```

--------------------------------

### Install STPSF with pip

Source: https://stpsf.readthedocs.io/en/latest/_sources/installation.rst.txt

Standard installation command for STPSF and its dependencies from the Python Package Index.

```bash
$ pip install --upgrade stpsf
[... progress report ...]

Successfully installed stpsf
```

--------------------------------

### Set up NIRCam instrument instance

Source: https://stpsf.readthedocs.io/en/latest/jwst_measured_opds.html

Instantiates a NIRCam instrument, sets the filter to F200W, selects detector NRCB2, and sets the detector position to (1024, 1024). This is the initial setup required before loading wavefront OPDs.

```python
nrc = stpsf.NIRCam()
nrc.filter='F200W'

nrc.detector = 'NRCB2'
nrc.detector_position = (1024,1024)
```

--------------------------------

### Import STPSF

Source: https://stpsf.readthedocs.io/en/latest/webbpsf_to_stpsf.html

Preferred transition method: import STPSF and replace all WebbPSF calls with STPSF. Requires installing STPSF, downloading stpsf-data-LATEST.tar.gz, and setting the STPSF_PATH environment variable.

```python
import stpsf

```

--------------------------------

### Define time range for WFE retrieval

Source: https://stpsf.readthedocs.io/en/latest/jwst_iec_wfe.html

Defines a time range using `astropy.time.Time` and `numpy.arange` with `astropy.units.minute` to create an array of 60 times starting from the given start time.

```python
tstart = astropy.time.Time('2022-07-10T16:00:00')

trange = tstart + np.arange(60) * astropy.units.minute

```

--------------------------------

### Initialize WFI and generate PSF grid

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/stpsf_core.html

Example of initializing the WFI instrument, setting filter and detector properties, and generating a PSF grid.

```python
wfi = stpsf.WFI()
wfi.filter = "Z087"
wfi.detector = "WFI02"
grid = wfi.psf_grid(all_detectors=False, oversample=5, fov_pixels=101)
```

--------------------------------

### Download example NIRCam observation

Source: https://stpsf.readthedocs.io/en/latest/jwst_psf_subtraction.html

Downloads the example F356W NIRCam observation from the Wavefront Sensing Maintenance program (PID 2725, obs 484). The file is cached locally.

```python
file = 'jw02725-o484_t097_nircam_clear-f356w-nrcalong_wfscmb-04.fits'
mast_retrieve_files(file)
```

--------------------------------

### Install STPSF and POPPY development versions via pip

Source: https://stpsf.readthedocs.io/en/latest/_sources/installation.rst.txt

Use this command to install the current development versions of STPSF and POPPY directly from their respective GitHub repositories. This creates local clones in a ./src directory.

```bash
$ pip install -e git+https://github.com/spacetelescope/poppy.git#egg=poppy \
   -e git+https://github.com/spacetelescope/stpsf.git#egg=stpsf
```

--------------------------------

### stpsf.setup_logging(level='INFO', filename=None)

Source: https://stpsf.readthedocs.io/en/latest/api/stpsf.setup_logging.html

Configures logging for stpsf and poppy, allowing selection of log detail level and output to screen and/or file. This is a convenience wrapper to Python's built-in logging package.

```APIDOC
## stpsf.setup_logging(level='INFO', filename=None)

### Description
Allows selection of logging detail and output locations (screen and/or file). This is a convenience wrapper to Python's built-in logging package, as used by `stpsf` and `poppy`. By default, this sets up log messages to be written to the screen, but the user can also request logging to a file.

### Method
Function call

### Endpoint
stpsf.setup_logging(level='INFO', filename=None)

### Parameters
- **level** (str) - Optional - Name of log output to show. Defaults to 'INFO', set to 'DEBUG' for more extensive messages, or to 'WARN' or 'ERROR' for fewer.
- **filename** (str) - Optional - Filename to write the log output to. If not set, output will just be displayed on screen. (Default: None)

### Request Example
python
>>> stpsf.setup_logging(filename='stpsflog.txt')


### Response
No return value. The function configures logging settings.

### Response Example
No response body. The function configures logging settings.

### Notes
- Editing the STPSF config file to set `autoconfigure_logging = True` (and any of the logging settings you wish to persist) instructs STPSF to apply your settings on import. (This is not done by default in case you have configured `logging` yourself and don't wish to overwrite your configuration.)
- For more advanced log handling, see the Python logging module's own documentation.

### Examples
python
>>> stpsf.setup_logging(filename='stpsflog.txt')

This will save all log messages to 'stpsflog.txt' in the current directory. If you later start another copy of stpsf in a different directory, that session will also write to 'stpsflog.txt' in _that_ directory. Alternatively you can specify a fully qualified absolute path to save all your logs to one specific file.

python
>>> stpsf.setup_logging(level='WARN')

This will show only WARNING or ERROR messages on screen, and not save any logs to files at all (since the filename argument is None).
```

--------------------------------

### NIRCam Coronagraph Shift

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/stpsf_core.html

Example of setting coronagraph shifts for NIRCam simulations.

```python
nc.options['coron_shift_x'] = 3  # Shifts mask 3" to right, equivalent to source 3" to left.
```

--------------------------------

### setup_logging function

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/utils.html

Convenience wrapper to Python's logging package for stpsf and poppy. Configures screen and optional file logging. Default level is 'INFO'; set to 'DEBUG', 'WARN', or 'ERROR' for different verbosity. If filename is None, no file logging is set up.

```python
[docs]
def setup_logging(level='INFO', filename=None):
    """Allows selection of logging detail and output locations
    (screen and/or file)

    This is a convenience wrapper to Python's built-in logging package,
    as used by `stpsf` and `poppy`. By default, this sets up log
    messages to be written to the screen, but the user can also
    request logging to a file.

    Editing the STPSF config file to set `autoconfigure_logging = True`
    (and any of the logging settings you wish to persist) instructs
    STPSF to apply your settings on import. (This is not
    done by default in case you have configured `logging` yourself
    and don't wish to overwrite your configuration.)

    For more advanced log handling, see the Python logging module's
    own documentation.

    Parameters
    ----------
    level : str
        Name of log output to show. Defaults to 'INFO', set to 'DEBUG'
        for more extensive messages, or to 'WARN' or 'ERROR' for fewer.
    filename : str, optional
        Filename to write the log output to. If not set, output will
        just be displayed on screen. (Default: None)

    Examples
    --------

    >>> stpsf.setup_logging(filename='stpsflog.txt')

    This will save all log messages to 'stpsflog.txt' in the current
    directory. If you later start another copy of stpsf in a
    different directory, that session will also write to
    'stpsflog.txt' in *that* directory. Alternatively you can specify
    a fully qualified absolute path to save all your logs to one
    specific file.

    >>> stpsf.setup_logging(level='WARN')

    This will show only WARNING or ERROR messages on screen, and not
    save any logs to files at all (since the filename argument is None)
    """
```

--------------------------------

### specFromSpectralType

Source: https://stpsf.readthedocs.io/en/latest/api_reference.html

Gets synphot Spectrum object from a user-friendly spectral type string.

```APIDOC
## specFromSpectralType

### Description
Get synphot Spectrum object from a user-friendly spectral type string.

### Method
Function

### Signature
`specFromSpectralType(sptype[, return_list, ...])`

### Parameters
- `sptype` (string) - Spectral type string.
- `return_list` (optional) - Whether to return a list.
- Additional parameters as supported by the function.

### Returns
Returns a synphot Spectrum object (or list of objects).
```

--------------------------------

### STPSF Module Initialization and Configuration

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf.html

This snippet contains the package-level setup, including the minimum Python version check, the definition of the Conf configuration class, and the import of core instrument classes and utility functions.

```python
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
STPSF: Simulated Point Spread Functions for the James Webb Space Telescope
----------------------------------------------------------------------------

STPSF produces simulated PSFs for the James Webb Space Telescope, NASA's next
flagship infrared space telescope. STPSF can simulate images for any of the
four science instruments plus the fine guidance sensor, including both direct
imaging and coronagraphic modes.

Developed by Marshall Perrin and collaborators at STScI, 2010-2018.

Documentation can be found online at https://stpsf.readthedocs.io/
"""

import sys
from astropy import config as _config

try:
    from .version import __version__
except ImportError:
    __version__ = ""

__minimum_python_version__ = "3.10"




[docs]
class UnsupportedPythonError(Exception):
    pass




if sys.version_info < tuple(
    (int(val) for val in __minimum_python_version__.split("."))
):
    raise UnsupportedPythonError(
        "stpsf does not support Python < {}".format(__minimum_python_version__)
    )


# This tuple gives the *minimum* version of the STPSF data package
# required. If changes to the code and data mean STPSF won't work
# properly with an old data package, increment this version number.
# (It's checked against $STPSF_DATA/version.txt)
DATA_VERSION_MIN = (2, 1, 0)




[docs]
class Conf(_config.ConfigNamespace):
    """
    Configuration parameters for `stpsf`.
    """

    default_oversampling = _config.ConfigItem(
        4,
        "Default "
        + "oversampling factor: number of times more finely sampled than "
        + "an integer pixel for the grid spacing in the PSF calculation.",
    )

    default_output_mode = _config.ConfigItem(
        "both",
        "Should output include the oversampled PSF, a copy rebinned onto the integer detector spacing, or both?\
        Options: 'oversampled','detector','both' ",
    )
    default_fov_arcsec = _config.ConfigItem(
        5.0, "Default field of view size, in arcseconds per side of the square "
    )

    # Should be package settings:
    STPSF_PATH = _config.ConfigItem(
        "from_environment_variable",
        "Directory path to data files required for STPSF calculations, such as OPDs and filter transmissions.\
        This will be overridden by the environment variable $STPSF_PATH, if present.",
    )
    autoconfigure_logging = _config.ConfigItem(
        False,
        "Should STPSF configure logging for itself and POPPY? This adds handlers that report "
        "calculation progress and information",
    )
    logging_level = _config.ConfigItem(
        ["INFO", "DEBUG", "WARN", "ERROR", "CRITICAL", "NONE"],
        # (the default value is the first item in the options list)
        "Desired logging level for STPSF optical calculations.",
    )
    logging_filename = _config.ConfigItem(
        "none", "Desired filename to save log messages to."
    )
    logging_format_screen = _config.ConfigItem(
        "[%(name)7s] %(message)s", "Format for lines logged to the screen."
    )
    logging_format_file = _config.ConfigItem(
        "%(asctime)s [%(name)s:%(levelname)s] %(filename)s:%(lineno)d: %(message)s",
        "Format for lines logged to a file.",
    )




conf = Conf()

from . import utils  # noqa - must go after config
from . import trending  # noqa - must go after config
from .utils import setup_logging, restart_logging, system_diagnostic, measure_strehl  # noqa - must go after config

from poppy import (  # noqa
    display_psf,
    display_psf_difference,
    display_ee,
    measure_ee,
    display_profiles,
    radial_profile,
    measure_radial,
    measure_fwhm,
    measure_sharpness,
    measure_centroid,
    specFromSpectralType,
    fwcentroid,
)

from .stpsf_core import (  # noqa
    instrument,
    SpaceTelescopeInstrument,
    JWInstrument,
    NIRCam,
    NIRISS,
    NIRSpec,
    MIRI,
    FGS,
)

from .opds import enable_adjustable_ote  # noqa

from .roman import WFI  # noqa

from .match_data import setup_sim_to_match_file  # noqa
```

--------------------------------

### Colorbar output from OPD plot

Source: https://stpsf.readthedocs.io/en/latest/field_dependence/multifield_documentation.html

Output from the colorbar command in the OPD plotting example.

```text
<matplotlib.colorbar.Colorbar at 0x11d622f90>
```

--------------------------------

### Show only warnings and errors with stpsf.setup_logging

Source: https://stpsf.readthedocs.io/en/latest/api/stpsf.setup_logging.html

Calls stpsf.setup_logging with level='WARN' to display only WARNING or ERROR messages on screen. Since filename is None, no logs are saved to files.

```python
>>> stpsf.setup_logging(level='WARN')

```

--------------------------------

### List detectors and select a different detector

Source: https://stpsf.readthedocs.io/en/latest/_sources/roman.rst.txt

Shows how to list all available detectors and change the detector by assigning a new name to the 'detector' attribute. The example selects 'WFI03'.

```python
>>> wfi.detector_list
['WFI01', 'WFI02', 'WFI03', 'WFI04', 'WFI05', 'WFI06', 'WFI07', 'WFI08', 'WFI09', 'WFI10', 'WFI11', 'WFI12', 'WFI13', 'WFI14', 'WFI15', 'WFI16', 'WFI17', 'WFI18']
>>> wfi.detector = 'WFI03'
```

--------------------------------

### Configure Image Array with setup_image_array

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/opds.html

Applies tilts to telescope segments to arrange them in an image array configuration. Requires an OTE_Linear_Model_WSS instance.

```python
def setup_image_array(
    ote, radius=1, size=None, inverted=False, reset=False, verbose=False, acfs_only=False, guide_seg=None, guide_radius=10.0
):
    """
    Apply tilts to put the segments in an image array configuration.

    Parameters
    ----------
    ote : OTE_Linear_Model_WSS instance
        The telescope model to be adjusted. This will be modified by this function.
    radius : float
        Desired radius to B segments, in arcseconds as seen on the focal plane.
    size : string, optional
        Another way of specifying the image array size. Use one of 'small', 'medium', or
        'large' for the standard sizes used in OTE commissioning. Or 'cmimf' for the size
        used in Coarse MIMF, which is in between small and medium.
    guide_seg : string
        relevant mostly for coarse MIMF and image stacking. Kick out a segment to guide?
        The segment will be offset during coarse MIMF to its position desired during GA2, i.e.
        to its position in the large array.
    acfs_only : bool
        Only tilt the ACFs (applicable to JSC OTIS only)
    inverted : bool
        Invert the array
    reset : bool
        Discard any previously applied mirror moves if true
    verbose : bool
        Print more text about moves.
    """

    assert isinstance(ote, OTE_Linear_Model_WSS), 'First argument has to be a linear optical model instance.'

    nircam_pixelscale = 0.0311
    standard_sizes = {
        'small': 80 * nircam_pixelscale,
        'cmimf': 120 * nircam_pixelscale,
        'medium': 300 * nircam_pixelscale,
        'large': 812 * nircam_pixelscale,
    }

    if size is not None:
        radius = standard_sizes[size]

    # how many microradians of segment tilt per arcsecond of PSF motion?
    # note factor of 2 since reflection
    arcsec_urad = (1 * u.arcsec).to(u.urad).value / 2

    if reset:
        ote.reset()

    # Image Arrays used in flight
    size = radius * -1 if inverted else radius
    for i in range(1, 7):
        ote.move_seg_local('A' + str(i), xtilt=size * arcsec_urad / 2, delay_update=True)
        ote.move_seg_local('B' + str(i), xtilt=-size * arcsec_urad, delay_update=True)
        ote.move_seg_local('C' + str(i), ytilt=size * np.sqrt(3) / 2 * arcsec_urad, delay_update=True)

    if guide_seg is not None:
        # Undo the regular tilt for this segment, and then move it to
        # the side.
        if 'A' in guide_seg:
            xtilt = (-size + standard_sizes['large']) / 2 * arcsec_urad
            ytilt = 0
        elif 'B' in guide_seg:
            xtilt = -size * arcsec_urad
            ytilt = guide_radius * arcsec_urad
        else:
            ytilt = (size * np.sqrt(3) / 2 + guide_radius) * arcsec_urad
            xtilt = 0
        ote.move_seg_local(guide_seg, xtilt=xtilt, ytilt=ytilt, delay_update=True)

    ote.update_opd(verbose=verbose)
```

--------------------------------

### Initialize NIRCam pupil

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/stpsf_core.html

Example of initializing a NIRCam object and setting a single segment pupil.

```python
nc = stpsf.NIRCam()
nc.pupil = stpsf.one_segment_pupil('B1')
```

--------------------------------

### NIRCam Coronagraph Bar Offset

Source: https://stpsf.readthedocs.io/en/latest/_modules/stpsf/stpsf_core.html

Example of setting a bar offset for NIRCam coronagraph simulations.

```python
nc.image_mask = 'MASKLWB'
nc.options['bar_offset'] = 3  # 3 arcseconds towards the right (narrow end on module A)
```
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