emccd-detect 2.3.0__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-2.5.0/PKG-INFO

@@ -0,0 +1,72 @@
+Metadata-Version: 2.4
+Name: emccd_detect
+Version: 2.5.0
+Summary: EMCCD detector image simulation
+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
+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
+
+Given an input fluxmap, emccd_detect will return a simulated EMCCD detector image.  Website:  (<https://github.com/roman-corgi/emccd_detect/tree/master/emccd_detect>)
+
+
+# Version
+
+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
+### Installing
+
+This package requires Python version 3.6 or higher.  If the user wants the ability to apply charge transfer inefficiency (CTI) to detector frames using the optional tool (older version of arcticpy which is pure Python) provided in emccd\_detect, then the Python version should be >=3.6 and <=3.9.  If the newer version of arcticpy (wrapper around C++ code) is installed, there is no upper limit restriction for Python version. For installation instructions and documentation for the newer arcticpy, see <https://github.com/jkeger/arctic>. emccd\_detect works apart from arcticpy and does not require it.
+
+emccd\_detect is available on PyPI.org, so the following command will install the module (without CTI capabilities):
+
+	pip install emccd-detect
+
+To install emccd\_detect instead from this package download, after downloading, navigate to the emccd\_detect directory where setup.py is located and use
+
+	pip install .
+
+This will install emccd\_detect and its dependencies, which are as follows:
+
+* astropy
+* matplotlib
+* numpy
+* scipy
+* pynufft==2020.0.0
+* pyyaml
+
+To optionally implement CTI capabilities with the pure-Python arcticpy, navigate to the arcticpy directory (<https://github.com/roman-corgi/emccd_detect/tree/master/arcticpy_folder>), and there will be a file called setup.py in that directory.  Use
+
+	pip install .
+
+This will install arcticpy version 1.0.  See (<https://github.com/jkeger/arcticpy/tree/row_wise/arcticpy>) for documentation.  If
+you have Python>3.9, the CTI functionality will not work if you are using the arcticpy installation that was included with this emccd_detect package, but everything else will work fine.
+
+
+### Usage
+
+For an example of how to use emccd\_detect, see example_script.py.
+
+
+## Authors
+
+* Bijan Nemati (<bijan.nemati@tellus1.com>)
+* Sam Miller (<sam.miller@uah.edu>)
+* Kevin Ludwick (<kevin.ludwick@uah.edu>)
+

emccd_detect-2.5.0/README.md

@@ -0,0 +1,53 @@
+# EMCCD Detect
+
+Given an input fluxmap, emccd_detect will return a simulated EMCCD detector image.  Website:  (<https://github.com/roman-corgi/emccd_detect/tree/master/emccd_detect>)
+
+
+# Version
+
+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
+### Installing
+
+This package requires Python version 3.6 or higher.  If the user wants the ability to apply charge transfer inefficiency (CTI) to detector frames using the optional tool (older version of arcticpy which is pure Python) provided in emccd\_detect, then the Python version should be >=3.6 and <=3.9.  If the newer version of arcticpy (wrapper around C++ code) is installed, there is no upper limit restriction for Python version. For installation instructions and documentation for the newer arcticpy, see <https://github.com/jkeger/arctic>. emccd\_detect works apart from arcticpy and does not require it.
+
+emccd\_detect is available on PyPI.org, so the following command will install the module (without CTI capabilities):
+
+	pip install emccd-detect
+
+To install emccd\_detect instead from this package download, after downloading, navigate to the emccd\_detect directory where setup.py is located and use
+
+	pip install .
+
+This will install emccd\_detect and its dependencies, which are as follows:
+
+* astropy
+* matplotlib
+* numpy
+* scipy
+* pynufft==2020.0.0
+* pyyaml
+
+To optionally implement CTI capabilities with the pure-Python arcticpy, navigate to the arcticpy directory (<https://github.com/roman-corgi/emccd_detect/tree/master/arcticpy_folder>), and there will be a file called setup.py in that directory.  Use
+
+	pip install .
+
+This will install arcticpy version 1.0.  See (<https://github.com/jkeger/arcticpy/tree/row_wise/arcticpy>) for documentation.  If
+you have Python>3.9, the CTI functionality will not work if you are using the arcticpy installation that was included with this emccd_detect package, but everything else will work fine.
+
+
+### Usage
+
+For an example of how to use emccd\_detect, see example_script.py.
+
+
+## Authors
+
+* Bijan Nemati (<bijan.nemati@tellus1.com>)
+* Sam Miller (<sam.miller@uah.edu>)
+* Kevin Ludwick (<kevin.ludwick@uah.edu>)
+

{emccd_detect-2.3.0 → emccd_detect-2.5.0}/emccd_detect/__init__.py

@@ -1,2 +1,2 @@
 # -*- coding: utf-8 -*-
-__version__ = '2.3.0'
+__version__ = '2.5.0'

{emccd_detect-2.3.0 → emccd_detect-2.5.0}/emccd_detect/emccd_detect.py

@@ -6,13 +6,14 @@ 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
 from emccd_detect.nonlinearity import apply_relgains
 from emccd_detect.util.read_metadata_wrapper import MetadataWrapper
 try:
-    from arcticpy import add_cti, CCD, ROE, Trap, TrapInstantCapture
+    from arcticpy import add_cti, CCD, ROE, TrapInstantCapture
 except:
     pass
 
@@ -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
@@ -92,14 +101,18 @@ 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.ccd = None
-        self.roe = None
-        self.traps = None
-        self.express = None
-        self.offset = None
-        self.window_range = None
+        self.parallel_ccd = None
+        self.parallel_roe = None
+        self.parallel_traps = None
+        self.parallel_express = None
+        self.serial_ccd = None
+        self.serial_roe = None
+        self.serial_traps = None
+        self.serial_express = None
+     
 
         # Placeholders for derived values
         self.mean_expected_rate = None
@@ -123,36 +136,72 @@ class EMCCDDetectBase:
     try:
         def update_cti(
             self,
-            ccd=None,
-            roe=None,
-            traps=None,
-            express=1,
-            offset=0,
-            window_range=None
+            parallel_ccd=None,
+            parallel_roe=None,
+            parallel_traps=None,
+            parallel_express=1,
+            serial_ccd=None,
+            serial_roe=None,
+            serial_traps=None,
+            serial_express=1,
+            parallel=True, 
+            serial=True,
+            **kwargs # any other arguments that arcticpy.add_cti() might accept
         ):
+            '''See arcticpy documentation for details on parameters. Any arguments 
+            not explicitly listed here can be handed to arcticpy.add_cti() via
+            kwargs.  
+            
+            Parallel and serial CTI can each be switched on or off via the 
+            "parallel" and "serial" arguments of this function.  True means that 
+            type of CTI is simulated.  Both are True by default.'''
             # Update parameters
-            self.ccd = ccd
-            self.roe = roe
-            self.traps = traps
-
-            self.express = express
-            self.offset = offset
-            self.window_range = window_range
+            self.parallel_ccd = parallel_ccd
+            self.parallel_roe = parallel_roe
+            self.parallel_traps = parallel_traps
+            self.parallel_express = parallel_express
+            self.serial_ccd = serial_ccd
+            self.serial_roe = serial_roe
+            self.serial_traps = serial_traps
+            self.serial_express = serial_express
+            self.kwargs = kwargs
+            self.parallel = parallel
+            self.serial = serial
 
             # Instantiate defaults for any class instances not provided
-            if self.ccd is None:
-                self.ccd = CCD()
-            if roe is None:
-                self.roe = ROE()
-            if traps is None:
+
+            if parallel_ccd is None:
+                self.parallel_ccd = CCD()
+            if parallel_roe is None:
+                self.parallel_roe = ROE()
+            if parallel_traps is None:
                 #self.traps = [Trap()]
-                self.traps = [TrapInstantCapture()]
+                self.parallel_traps = [TrapInstantCapture()]
+            if self.parallel is False: # overrides
+                self.parallel_ccd = None
+                self.parallel_roe = None
+                self.parallel_traps = None
+
+            if serial_ccd is None:
+                self.serial_ccd = CCD()
+            if serial_roe is None:
+                self.serial_roe = ROE()
+            if serial_traps is None:
+                self.serial_traps = [TrapInstantCapture()]
+            if self.serial is False: #overrides
+                self.serial_ccd = None
+                self.serial_roe = None
+                self.serial_traps = None
 
         def unset_cti(self):
+            '''This turns off all CTI implementation.'''
             # Remove CTI simulation
-            self.ccd = None
-            self.roe = None
-            self.traps = None
+            self.parallel_ccd = None
+            self.parallel_roe = None
+            self.parallel_traps = None
+            self.serial_ccd = None
+            self.serial_roe = None
+            self.serial_traps = None
     except:
         pass
 
@@ -207,6 +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),
@@ -225,16 +311,26 @@ class EMCCDDetectBase:
 
     def clock_parallel(self, actualized_e):
         # Only add CTI if update_cti has been called
-        if self.ccd is not None and self.roe is not None and self.traps is not None:
-            parallel_counts = add_cti(
-                actualized_e.copy(),
-                parallel_roe=self.roe,
-                parallel_ccd=self.ccd,
-                parallel_traps=self.traps,
-                parallel_express=self.express,
-                parallel_offset=self.offset,
-                parallel_window_range=self.window_range
-            )
+        if self.parallel_ccd is not None and self.parallel_roe is not None and self.parallel_traps is not None:
+            try:
+                parallel_counts = add_cti(
+                    actualized_e.copy(),
+                    parallel_roe=self.parallel_roe,
+                    parallel_ccd=self.parallel_ccd,
+                    parallel_traps=self.parallel_traps,
+                    parallel_express=self.parallel_express,
+                    **self.kwargs
+                )
+            except:
+                parallel_counts = add_cti(
+                    actualized_e.copy(),
+                    parallel_roe=self.parallel_roe,
+                    parallel_ccd=self.parallel_ccd,
+                    parallel_traps=self.parallel_traps,
+                    parallel_express=self.parallel_express,
+                    parallel_window_range=0,
+                    **self.kwargs
+                )
         else:
             parallel_counts = actualized_e
 
@@ -242,12 +338,37 @@ class EMCCDDetectBase:
 
     def clock_serial(self, actualized_e_full, empty_element_m):
         # Actualize cic electrons in prescan and overscan pixels
-        # XXX Another place where we are fudging a little
+        # XXX Another place where we are fudging a little as far as the order of operations(?)
         actualized_e_full[empty_element_m] = np.random.poisson(actualized_e_full[empty_element_m]
                                                                + self.cic)
-        # XXX Call arcticpy here
+        
+        # add serial CTI; the addition of CIC (serial and parallel) is really 
+        # *during* the addition of CTI, but this corrective effect would not be very significant 
+        if self.serial_ccd is not None and self.serial_roe is not None and self.serial_traps is not None:
+            try:
+                cti_actualized_e_full = add_cti(
+                        actualized_e_full.copy(),
+                        serial_roe=self.serial_roe,
+                        serial_ccd=self.serial_ccd,
+                        serial_traps=self.serial_traps,
+                        serial_express=self.serial_express,
+                        **self.kwargs
+                    )
+            except:
+                cti_actualized_e_full = add_cti(
+                        actualized_e_full.copy(),
+                        serial_roe=self.serial_roe,
+                        serial_ccd=self.serial_ccd,
+                        serial_traps=self.serial_traps,
+                        serial_express=self.serial_express,
+                        serial_window_range=0,
+                        **self.kwargs
+                    )
+        else:
+            cti_actualized_e_full = actualized_e_full
+
         # Flatten row by row
-        actualized_e_full_flat = actualized_e_full.ravel()
+        actualized_e_full_flat = cti_actualized_e_full.ravel()
 
         # Clock electrons through serial register elements
         serial_counts = self._serial_register_elements(actualized_e_full_flat)
@@ -429,7 +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
@@ -445,7 +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.
@@ -458,15 +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.,
@@ -474,11 +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:
@@ -489,13 +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,
@@ -510,7 +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):
@@ -613,6 +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
 
 
@@ -704,7 +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-2.3.0 → emccd_detect-2.5.0}/emccd_detect/nonlinearity.py

@@ -4,6 +4,8 @@ pixel of a frame.
 
 Relative gain is dependent on both the detector gain and the dn count
 value of a given pixel.
+
+Adapted from https://github.com/roman-corgi/cgi_iit_drp/blob/main/proc_cgi_frame_NTR/proc_cgi_frame/gsw_nonlin.py.
 """
 
 import numpy as np

{emccd_detect-2.3.0 → 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-2.3.0 → 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-2.3.0 → 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-2.5.0/emccd_detect.egg-info/PKG-INFO

@@ -0,0 +1,72 @@
+Metadata-Version: 2.4
+Name: emccd_detect
+Version: 2.5.0
+Summary: EMCCD detector image simulation
+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
+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
+
+Given an input fluxmap, emccd_detect will return a simulated EMCCD detector image.  Website:  (<https://github.com/roman-corgi/emccd_detect/tree/master/emccd_detect>)
+
+
+# Version
+
+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
+### Installing
+
+This package requires Python version 3.6 or higher.  If the user wants the ability to apply charge transfer inefficiency (CTI) to detector frames using the optional tool (older version of arcticpy which is pure Python) provided in emccd\_detect, then the Python version should be >=3.6 and <=3.9.  If the newer version of arcticpy (wrapper around C++ code) is installed, there is no upper limit restriction for Python version. For installation instructions and documentation for the newer arcticpy, see <https://github.com/jkeger/arctic>. emccd\_detect works apart from arcticpy and does not require it.
+
+emccd\_detect is available on PyPI.org, so the following command will install the module (without CTI capabilities):
+
+	pip install emccd-detect
+
+To install emccd\_detect instead from this package download, after downloading, navigate to the emccd\_detect directory where setup.py is located and use
+
+	pip install .
+
+This will install emccd\_detect and its dependencies, which are as follows:
+
+* astropy
+* matplotlib
+* numpy
+* scipy
+* pynufft==2020.0.0
+* pyyaml
+
+To optionally implement CTI capabilities with the pure-Python arcticpy, navigate to the arcticpy directory (<https://github.com/roman-corgi/emccd_detect/tree/master/arcticpy_folder>), and there will be a file called setup.py in that directory.  Use
+
+	pip install .
+
+This will install arcticpy version 1.0.  See (<https://github.com/jkeger/arcticpy/tree/row_wise/arcticpy>) for documentation.  If
+you have Python>3.9, the CTI functionality will not work if you are using the arcticpy installation that was included with this emccd_detect package, but everything else will work fine.
+
+
+### Usage
+
+For an example of how to use emccd\_detect, see example_script.py.
+
+
+## Authors
+
+* Bijan Nemati (<bijan.nemati@tellus1.com>)
+* Sam Miller (<sam.miller@uah.edu>)
+* Kevin Ludwick (<kevin.ludwick@uah.edu>)
+

{emccd_detect-2.3.0 → emccd_detect-2.5.0}/emccd_detect.egg-info/SOURCES.txt

@@ -1,4 +1,6 @@
+LICENSE.txt
 README.md
+pyproject.toml
 setup.py
 emccd_detect/__init__.py
 emccd_detect/cosmics.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-2.3.0/PKG-INFO

@@ -1,69 +0,0 @@
-Metadata-Version: 2.1
-Name: emccd_detect
-Version: 2.3.0
-Summary: EMCCD detector image simulation
-Home-page: 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
-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
-Requires-Dist: astropy
-Requires-Dist: matplotlib
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: pynufft==2020.0.0
-Requires-Dist: pyyaml
-
-# EMCCD Detect
-
-Given an input fluxmap, emccd_detect will return a simulated EMCCD detector image.  Website:  (<https://github.com/roman-corgi/emccd_detect/tree/master/emccd_detect>)
-
-
-# Version
-
-The latest version of emccd\_detect is 2.3.0.
-
-
-## Getting Started
-### Installing
-
-This package requires Python version 3.6 or higher.  If the user wants the ability to apply charge transfer inefficiency (CTI) to detector frames using the optional tool provided in emccd\_detect, then the Python version should be >=3.6 and <=3.9.
-
-To install emccd\_detect, navigate to the emccd\_detect directory where setup.py is located and use
-
-	pip install .
-
-This will install emccd\_detect and its dependencies, which are as follows:
-
-* astropy
-* matplotlib
-* numpy
-* scipy
-* pynufft==2020.0.0
-* pyyaml
-
-To optionally implement CTI capabilities, navigate to the arcticpy directory (<https://github.com/roman-corgi/emccd_detect/tree/master/arcticpy_folder>), and there will be a file called setup.py in that directory.  Use
-
-	pip install .
-
-This will install arcticpy version 1.0, which is an older version of arcticpy which runs purely on Python (<https://github.com/jkeger/arcticpy/tree/row_wise/arcticpy>).  If
-you have Python>=3.10, the CTI functionality will not work if you are using the arcticpy installation that was included with this emccd_detect package, but everything else will work fine.
-
-
-### Usage
-
-For an example of how to use emccd\_detect, see example_script.py.
-
-
-## Authors
-
-* Bijan Nemati (<bijan.nemati@tellus1.com>)
-* Sam Miller (<sam.miller@uah.edu>)
-* Kevin Ludwick (<kevin.ludwick@uah.edu>)
-

emccd_detect-2.3.0/README.md

@@ -1,47 +0,0 @@
-# EMCCD Detect
-
-Given an input fluxmap, emccd_detect will return a simulated EMCCD detector image.  Website:  (<https://github.com/roman-corgi/emccd_detect/tree/master/emccd_detect>)
-
-
-# Version
-
-The latest version of emccd\_detect is 2.3.0.
-
-
-## Getting Started
-### Installing
-
-This package requires Python version 3.6 or higher.  If the user wants the ability to apply charge transfer inefficiency (CTI) to detector frames using the optional tool provided in emccd\_detect, then the Python version should be >=3.6 and <=3.9.
-
-To install emccd\_detect, navigate to the emccd\_detect directory where setup.py is located and use
-
-	pip install .
-
-This will install emccd\_detect and its dependencies, which are as follows:
-
-* astropy
-* matplotlib
-* numpy
-* scipy
-* pynufft==2020.0.0
-* pyyaml
-
-To optionally implement CTI capabilities, navigate to the arcticpy directory (<https://github.com/roman-corgi/emccd_detect/tree/master/arcticpy_folder>), and there will be a file called setup.py in that directory.  Use
-
-	pip install .
-
-This will install arcticpy version 1.0, which is an older version of arcticpy which runs purely on Python (<https://github.com/jkeger/arcticpy/tree/row_wise/arcticpy>).  If
-you have Python>=3.10, the CTI functionality will not work if you are using the arcticpy installation that was included with this emccd_detect package, but everything else will work fine.
-
-
-### Usage
-
-For an example of how to use emccd\_detect, see example_script.py.
-
-
-## Authors
-
-* Bijan Nemati (<bijan.nemati@tellus1.com>)
-* Sam Miller (<sam.miller@uah.edu>)
-* Kevin Ludwick (<kevin.ludwick@uah.edu>)
-

emccd_detect-2.3.0/emccd_detect.egg-info/PKG-INFO

@@ -1,69 +0,0 @@
-Metadata-Version: 2.1
-Name: emccd_detect
-Version: 2.3.0
-Summary: EMCCD detector image simulation
-Home-page: 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
-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
-Requires-Dist: astropy
-Requires-Dist: matplotlib
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: pynufft==2020.0.0
-Requires-Dist: pyyaml
-
-# EMCCD Detect
-
-Given an input fluxmap, emccd_detect will return a simulated EMCCD detector image.  Website:  (<https://github.com/roman-corgi/emccd_detect/tree/master/emccd_detect>)
-
-
-# Version
-
-The latest version of emccd\_detect is 2.3.0.
-
-
-## Getting Started
-### Installing
-
-This package requires Python version 3.6 or higher.  If the user wants the ability to apply charge transfer inefficiency (CTI) to detector frames using the optional tool provided in emccd\_detect, then the Python version should be >=3.6 and <=3.9.
-
-To install emccd\_detect, navigate to the emccd\_detect directory where setup.py is located and use
-
-	pip install .
-
-This will install emccd\_detect and its dependencies, which are as follows:
-
-* astropy
-* matplotlib
-* numpy
-* scipy
-* pynufft==2020.0.0
-* pyyaml
-
-To optionally implement CTI capabilities, navigate to the arcticpy directory (<https://github.com/roman-corgi/emccd_detect/tree/master/arcticpy_folder>), and there will be a file called setup.py in that directory.  Use
-
-	pip install .
-
-This will install arcticpy version 1.0, which is an older version of arcticpy which runs purely on Python (<https://github.com/jkeger/arcticpy/tree/row_wise/arcticpy>).  If
-you have Python>=3.10, the CTI functionality will not work if you are using the arcticpy installation that was included with this emccd_detect package, but everything else will work fine.
-
-
-### Usage
-
-For an example of how to use emccd\_detect, see example_script.py.
-
-
-## Authors
-
-* Bijan Nemati (<bijan.nemati@tellus1.com>)
-* Sam Miller (<sam.miller@uah.edu>)
-* Kevin Ludwick (<kevin.ludwick@uah.edu>)
-

emccd_detect-2.3.0/emccd_detect.egg-info/top_level.txt

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

emccd_detect-2.3.0/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=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'
-    ]
-)