emccd-detect 2.4.0__tar.gz → 2.5.0__tar.gz

emccd_detect-2.5.0/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Bijan Nemati, Sam Miller, and Kevin Ludwick
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/PKG-INFO

@@ -1,23 +1,21 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: emccd_detect
-Version: 2.4.0
+Version: 2.5.0
 Summary: EMCCD detector image simulation
-Author: Bijan Nemati, Sam Miller, Kevin Ludwick
-Author-email: bijan.nemati@tellus1.com, sam.miller@uah.edu, kevin.ludwick@uah.edu
+Author-email: Bijan Nemati <bijan.nemati@tellus1.com>, Sam Miller <sam.miller@uah.edu>, Kevin Ludwick <kevin.ludwick@uah.edu>
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
+License-File: LICENSE.txt
 Requires-Dist: astropy
 Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: pynufft==2020.0.0
 Requires-Dist: pyyaml
+Dynamic: license-file
 
 # EMCCD Detect
 
@@ -26,7 +24,9 @@ Given an input fluxmap, emccd_detect will return a simulated EMCCD detector imag
 
 # Version
 
-The latest version of emccd\_detect is 2.4.0.  Main differences from previous version: the ability to implement readout nonlinearity and the latest version of arcticpy for charge transfer inefficiency implementation.
+The latest version of emccd\_detect is 2.5.0.  Main differences from previous version, 2.4.0: 
+--the ability to implement smear due to exposure of some rows while others are being read out.  Credit for this smearing code: Peter Williams, Tellus1, 2024.
+--the ability to implement non-uniformity in pixel response via an input master flat.  Assumed to be a FITS file.
 
 
 ## Getting Started

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/README.md

@@ -5,7 +5,9 @@ Given an input fluxmap, emccd_detect will return a simulated EMCCD detector imag
 
 # Version
 
-The latest version of emccd\_detect is 2.4.0.  Main differences from previous version: the ability to implement readout nonlinearity and the latest version of arcticpy for charge transfer inefficiency implementation.
+The latest version of emccd\_detect is 2.5.0.  Main differences from previous version, 2.4.0: 
+--the ability to implement smear due to exposure of some rows while others are being read out.  Credit for this smearing code: Peter Williams, Tellus1, 2024.
+--the ability to implement non-uniformity in pixel response via an input master flat.  Assumed to be a FITS file.
 
 
 ## Getting Started

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect/__init__.py

@@ -1,2 +1,2 @@
 # -*- coding: utf-8 -*-
-__version__ = '2.4.0'
+__version__ = '2.5.0'

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect/emccd_detect.py

@@ -6,6 +6,7 @@ import warnings
 from pathlib import Path
 
 import numpy as np
+from astropy.io import fits
 
 from emccd_detect.cosmics import cosmic_hits, sat_tails
 from emccd_detect.rand_em_gain import rand_em_gain
@@ -54,7 +55,12 @@ class EMCCDDetectBase:
         inclusive.
     numel_gain_register : int
         Number of gain register elements. For eventually modeling partial CIC.
-
+    row_read_time : float
+        Time in seconds for each row to move into the first register (same as 
+        the time for each row to be clocked toward the register). This is used 
+        to simulate smear on the image due to clocking during the exposure to 
+        light.  Especially useful for shutterless EMCCDs.  If 0, no smear is 
+        simulated.
     """
     def __init__(
         self,
@@ -70,7 +76,8 @@ class EMCCDDetectBase:
         pixel_pitch,
         eperdn,
         nbits,
-        numel_gain_register
+        numel_gain_register,
+        row_read_time
     ):
         # Input checks
         if not isinstance(nbits, (int, np.integer)):
@@ -78,6 +85,8 @@ class EMCCDDetectBase:
         if nbits < 1 or nbits > 64:
             raise EMCCDDetectException('nbits must be between 1 and 64, '
                                        'inclusive')
+        if row_read_time < 0:
+            raise EMCCDDetectException('row_read_time must be >= 0 seconds.')
 
         self.em_gain = em_gain
         self.full_well_image = full_well_image
@@ -92,6 +101,7 @@ class EMCCDDetectBase:
         self.eperdn = eperdn
         self.nbits = nbits
         self.numel_gain_register = numel_gain_register
+        self.row_read_time = row_read_time
 
         # Placeholders for trap parameters
         self.parallel_ccd = None
@@ -246,6 +256,43 @@ class EMCCDDetectBase:
         return output_dn.reshape(actualized_e.shape)
 
     def integrate(self, fluxmap_full, frametime, exposed_pix_m):
+        # apply non-uniformity of pixel responsivity via master flat
+        if hasattr(self, 'flat_path'):
+            if self.flat_path is not None:
+                with fits.open(self.flat_path) as hdul:
+                    self.flat = hdul[1].data
+                if (self.flat < 0).any():
+                    raise EMCCDDetectException('Master flat must not contain '
+                                                'negative values.')
+                if self.flat.shape != fluxmap_full.shape:
+                    imaging_area_ones = np.ones_like(fluxmap_full)
+                    # Attempt to embed the flat within the 
+                    # imaging+shielded area
+                    self.flat_im = self.meta.embed_im(imaging_area_ones, 
+                                                    'image', self.flat.copy())
+                    if self.flat_im.shape != fluxmap_full.shape:
+                        raise EMCCDDetectException('Master flat shape must '
+                                                'agree with shape of fluxmap.')
+                    else:
+                        fluxmap_full *= self.flat_im
+                else:   
+                    fluxmap_full *= self.flat
+
+        # simulate smear to fluxmap
+        # credit for this smearing code: Peter Williams, Tellus1, 2024
+        # XXX Technically, smearing adds electrons to each pixel, which 
+        # increases the chance of charge capture for CTI, but simulating 
+        # this small effect would require hacking arCTIc.
+        smear = np.zeros_like(fluxmap_full)
+        m = len(smear)
+        for r in range(m):
+            columnsum = 0
+            for i in range(r+1):
+                columnsum = columnsum + self.row_read_time*fluxmap_full[i,:]
+            smear[r,:] = columnsum
+        
+        fluxmap_full = fluxmap_full + smear/frametime
+
         # Add cosmic ray effects
         # XXX Maybe change this to units of flux later
         cosm_actualized_e = cosmic_hits(np.zeros_like(fluxmap_full),
@@ -503,7 +550,7 @@ class EMCCDDetect(EMCCDDetectBase):
     full_well_image : float
         Image area full well capacity (e-). Defaults to 78000.
     full_well_serial : float
-        Serial (gain) register full well capacity (e-). Defaults to None.
+        Serial (gain) register full well capacity (e-). Defaults to 105000.
     dark_current: float
         Dark current rate (e-/pix/s). Defaults to 0.00031.
     cic : float
@@ -519,7 +566,7 @@ class EMCCDDetect(EMCCDDetectBase):
     pixel_pitch : float
         Distance between pixel centers (m). Defaults to 13e-6.
     eperdn : float
-        Electrons per dn. Defaults to None.
+        Electrons per dn. Defaults to 8.2.
     nbits : int
         Number of bits used by the ADC readout. Must be between 1 and 64,
         inclusive. Defaults to 14.
@@ -532,15 +579,28 @@ class EMCCDDetect(EMCCDDetectBase):
     nonlin_path : str
         Path of nonlinearity correction file.  See doc string of 
         nonlinearity.apply_relgains for details on the required 
-        format of the file.  If None, defaults to no application of 
-        nonlinearity.
+        format of the file.  If None, no application of 
+        nonlinearity is performed.  Defaults to None.
+    row_read_time : float
+        Time in seconds for each row to move into the first register (same as 
+        the time for each row to be clocked toward the register). This is used 
+        to simulate smear on the image due to clocking during the exposure to 
+        light.  Especially useful for shutterless EMCCDs.  If 0, no smear is 
+        simulated.  Defaults to 0 seconds.
+    flat_path : str
+        Path of master flat file.  Assumed to be a FITS file for which the flat
+        data resides in the first extension HDU.  The flat is assumed to be
+        of image-area shape (specified by the metadata from meta_path),
+        dark-subtracted, divided by k-gain, divided by EM gain, and desmeared. 
+        If the input is None, no application of pixel nonuniformity is 
+        performed.  Defaults to None.
 
     """
     def __init__(
         self,
         em_gain=1.,
         full_well_image=78000.,
-        full_well_serial=None,
+        full_well_serial=105000.,
         dark_current=0.00031,
         cic=0.016,
         read_noise=110.,
@@ -548,11 +608,13 @@ class EMCCDDetect(EMCCDDetectBase):
         qe=0.9,
         cr_rate=0.,
         pixel_pitch=13e-6,
-        eperdn=None,
+        eperdn=8.2,
         nbits=14,
         numel_gain_register=604,
         meta_path=None,
-        nonlin_path=None
+        nonlin_path=None,
+        row_read_time=0,  # seconds
+        flat_path=None
     ):
         # If no metadata file path specified, default to metadata.yaml in util
         if meta_path is None:
@@ -563,13 +625,8 @@ class EMCCDDetect(EMCCDDetectBase):
         self.meta_path = meta_path
         self.meta = MetadataWrapper(self.meta_path)
 
-        # Set defaults from metadata
-        if full_well_serial is None:
-            full_well_serial = self.meta.fwc
-        if eperdn is None:
-            eperdn = self.meta.eperdn
-
         self.nonlin_path = nonlin_path
+        self.flat_path = flat_path
 
         super().__init__(
             em_gain=em_gain,
@@ -584,7 +641,8 @@ class EMCCDDetect(EMCCDDetectBase):
             pixel_pitch=pixel_pitch,
             eperdn=eperdn,
             nbits=nbits,
-            numel_gain_register=numel_gain_register
+            numel_gain_register=numel_gain_register,
+            row_read_time=row_read_time
         )
 
     def sim_full_frame(self, fluxmap, frametime):
@@ -687,6 +745,12 @@ class EMCCDDetect(EMCCDDetectBase):
             Bias subtracted, gain divided frame in units of e-.
 
         """
+        if hasattr(self, 'nonlin_path'):
+            if self.nonlin_path is not None:
+                nonlin_factors = apply_relgains(frame_dn, self.em_gain, 
+                                                self.nonlin_path)
+                # correct fo nonlin by dividing
+                frame_dn = frame_dn/nonlin_factors
         return (frame_dn * self.eperdn - self.bias) / self.em_gain
 
 
@@ -778,7 +842,8 @@ def emccd_detect(
         pixel_pitch=pixel_pitch,
         eperdn=1.,
         nbits=64,
-        numel_gain_register=604
+        numel_gain_register=604,
+        row_read_time=0
     )
 
     return emccd.sim_sub_frame(fluxmap, frametime).astype(float)

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect/util/metadata.yaml

@@ -50,11 +50,4 @@ geom:
     cols: 56
     r0c0:
       - 0
-      - 2144
-eperdn: 8.2
-fwc: 105000 #serial
-sat_thresh: 0.99
-plat_thresh: 0.85
-cosm_filter: 2
-tail_filter: #5
-cic_thresh: #100
+      - 2144

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect/util/read_metadata.py

@@ -22,20 +22,6 @@ class Metadata(object):
         Data from metadata file.
     geom : SimpleNamespace
         Geometry specific data.
-    eperdn : float
-        Electrons per dn conversion factor (detector k gain).
-    fwc : float
-        Full well capacity of detector.
-    sat_thresh : float
-        Multiplication factor for fwc that determines saturated cosmic pixels.
-    plat_thresh : float
-        Multiplication factor for fwc that determines edges of cosmic plateu.
-    cosm_filter : int
-        Minimum length in pixels of cosmic plateus to be identified.
-    tail_filter : int
-        Moving median filter window size for cosmic tail subtraction.
-    cic_thresh : float
-        Multiplication factor for readnoise that determines beginning of cic.
 
     B Nemati and S Miller - UAH - 03-Aug-2018
 
@@ -48,13 +34,6 @@ class Metadata(object):
         self.frame_rows = self.data['frame_rows']
         self.frame_cols = self.data['frame_cols']
         self.geom = self.data['geom']
-        self.eperdn = self.data['eperdn']
-        self.fwc = self.data['fwc']
-        self.sat_thresh = self.data['sat_thresh']
-        self.plat_thresh = self.data['plat_thresh']
-        self.cosm_filter = self.data['cosm_filter']
-        self.tail_filter = self.data['tail_filter']
-        self.cic_thresh = self.data['cic_thresh']
 
     def get_data(self):
         """Read yaml data into dictionary."""

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect/util/read_metadata_wrapper.py

@@ -23,20 +23,6 @@ class MetadataWrapper(Metadata):
         Data from metadata file.
     geom : SimpleNamespace
         Geometry specific data.
-    eperdn : float
-        Electrons per dn conversion factor (detector k gain).
-    fwc : float
-        Full well capacity of detector.
-    sat_thresh : float
-        Multiplication factor for fwc that determines saturated cosmic pixels.
-    plat_thresh : float
-        Multiplication factor for fwc that determines edges of cosmic plateu.
-    cosm_filter : int
-        Minimum length in pixels of cosmic plateus to be identified.
-    tail_filter : int
-        Moving median filter window size for cosmic tail subtraction.
-    cic_thresh : float
-        Multiplication factor for readnoise that determines beginning of cic.
 
     """
 

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect.egg-info/PKG-INFO

@@ -1,23 +1,21 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: emccd_detect
-Version: 2.4.0
+Version: 2.5.0
 Summary: EMCCD detector image simulation
-Author: Bijan Nemati, Sam Miller, Kevin Ludwick
-Author-email: bijan.nemati@tellus1.com, sam.miller@uah.edu, kevin.ludwick@uah.edu
+Author-email: Bijan Nemati <bijan.nemati@tellus1.com>, Sam Miller <sam.miller@uah.edu>, Kevin Ludwick <kevin.ludwick@uah.edu>
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
+License-File: LICENSE.txt
 Requires-Dist: astropy
 Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: pynufft==2020.0.0
 Requires-Dist: pyyaml
+Dynamic: license-file
 
 # EMCCD Detect
 
@@ -26,7 +24,9 @@ Given an input fluxmap, emccd_detect will return a simulated EMCCD detector imag
 
 # Version
 
-The latest version of emccd\_detect is 2.4.0.  Main differences from previous version: the ability to implement readout nonlinearity and the latest version of arcticpy for charge transfer inefficiency implementation.
+The latest version of emccd\_detect is 2.5.0.  Main differences from previous version, 2.4.0: 
+--the ability to implement smear due to exposure of some rows while others are being read out.  Credit for this smearing code: Peter Williams, Tellus1, 2024.
+--the ability to implement non-uniformity in pixel response via an input master flat.  Assumed to be a FITS file.
 
 
 ## Getting Started

{emccd_detect-2.4.0 → emccd_detect-2.5.0}/emccd_detect.egg-info/SOURCES.txt

@@ -1,3 +1,4 @@
+LICENSE.txt
 README.md
 pyproject.toml
 setup.py

emccd_detect-2.5.0/emccd_detect.egg-info/top_level.txt

@@ -0,0 +1,4 @@
+data
+dist
+docs
+emccd_detect

emccd_detect-2.5.0/pyproject.toml

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "emccd_detect"
+version = "2.5.0"
+description = "EMCCD detector image simulation"
+readme = "README.md"
+authors = [
+  { name = "Bijan Nemati", email = "bijan.nemati@tellus1.com" },
+  { name = "Sam Miller", email = "sam.miller@uah.edu" },
+  { name = "Kevin Ludwick", email = "kevin.ludwick@uah.edu" },
+]
+license = { file = "LICENSE" }
+requires-python = ">=3.6"
+dependencies = [
+  "astropy",
+  "matplotlib",
+  "numpy",
+  "scipy",
+  "pynufft==2020.0.0",
+  "pyyaml",
+]
+
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Developers",
+  "Programming Language :: Python :: 3",
+]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+exclude = [
+  "arcticpy_folder",
+  "arcticpy_folder.*",
+  "arcticpy",
+  "arcticpy.*",
+]
+
+[tool.setuptools.package-data]
+"*" = ["metadata.yaml"]

emccd_detect-2.5.0/setup.py

@@ -0,0 +1,54 @@
+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()
+
+# # -*- coding: utf-8 -*-
+# from io import open
+# from os import path
+# from setuptools import setup, find_packages, find_namespace_packages
+# #import emccd_detect
+
+# here = path.abspath(path.dirname(__file__))
+
+# with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+#     long_description = f.read()
+
+# setup(
+#     name='emccd_detect',
+#     version='2.5.0', #emccd_detect.__version__,
+#     description='EMCCD detector image simulation',
+#     long_description=long_description,
+#     long_description_content_type='text/markdown',
+#     #url='https://github.jpl.nasa.gov/WFIRST-CGI/emccd_detect',
+#     author='Bijan Nemati, Sam Miller, Kevin Ludwick',
+#     author_email='bijan.nemati@tellus1.com, sam.miller@uah.edu, kevin.ludwick@uah.edu',
+#     classifiers=[
+#         'Development Status :: 4 - Beta',
+#         'Intended Audience :: Developers',
+#         'Programming Language :: Python :: 3',
+#         # 'Programming Language :: Python :: 3.6',
+#         # 'Programming Language :: Python :: 3.7',
+#         # 'Programming Language :: Python :: 3.8',
+#     ],
+#     #packages=find_namespace_packages('arcticpy.src', 'arcticpy.include'),
+#     packages=find_packages(exclude=["arcticpy_folder.*", "arcticpy_folder", "arcticpy.*", "arcticpy"]),
+#     #packages=find_namespace_packages(),
+#     #packages=['emccd_detect'],
+#     package_data={'': ['metadata.yaml']},
+#     include_package_data=True,
+#     #exclude_package_data={'':['arcticpy']},
+#     python_requires= '>=3.6',
+#     install_requires=[
+#         #'arcticpy @ git+https://github.com/jkeger/arcticpy@row_wise#egg=arcticpy',
+#         #'arcticpy @ git+https://github.com/jkeger/arcticpy.git',
+#         #'arcticpy @ git+https://github.com/jkeger/arctic.git',
+#         #'arctic',
+#         'astropy',
+#         'matplotlib',
+#         'numpy',
+#         'scipy',
+#         'pynufft==2020.0.0',
+#         'pyyaml'
+#     ]
+# )

emccd_detect-2.4.0/emccd_detect.egg-info/top_level.txt

@@ -1 +0,0 @@
-emccd_detect

emccd_detect-2.4.0/pyproject.toml

@@ -1,3 +0,0 @@
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"

emccd_detect-2.4.0/setup.py

@@ -1,49 +0,0 @@
-# -*- coding: utf-8 -*-
-from io import open
-from os import path
-from setuptools import setup, find_packages, find_namespace_packages
-#import emccd_detect
-
-here = path.abspath(path.dirname(__file__))
-
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
-
-setup(
-    name='emccd_detect',
-    version='2.4.0', #emccd_detect.__version__,
-    description='EMCCD detector image simulation',
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    #url='https://github.jpl.nasa.gov/WFIRST-CGI/emccd_detect',
-    author='Bijan Nemati, Sam Miller, Kevin Ludwick',
-    author_email='bijan.nemati@tellus1.com, sam.miller@uah.edu, kevin.ludwick@uah.edu',
-    classifiers=[
-        'Development Status :: 4 - Beta',
-        'Intended Audience :: Developers',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-    ],
-    #packages=find_namespace_packages('arcticpy.src', 'arcticpy.include'),
-    packages=find_packages(exclude=["arcticpy_folder.*", "arcticpy_folder", "arcticpy.*", "arcticpy"]),
-    #packages=find_namespace_packages(),
-    #packages=['emccd_detect'],
-    package_data={'': ['metadata.yaml']},
-    include_package_data=True,
-    #exclude_package_data={'':['arcticpy']},
-    python_requires= '>=3.6',
-    install_requires=[
-        #'arcticpy @ git+https://github.com/jkeger/arcticpy@row_wise#egg=arcticpy',
-        #'arcticpy @ git+https://github.com/jkeger/arcticpy.git',
-        #'arcticpy @ git+https://github.com/jkeger/arctic.git',
-        #'arctic',
-        'astropy',
-        'matplotlib',
-        'numpy',
-        'scipy',
-        'pynufft==2020.0.0',
-        'pyyaml'
-    ]
-)