emccd-detect 2.3.0__py3-none-any.whl → 2.4.0__py3-none-any.whl

emccd_detect/__init__.py

@@ -1,2 +1,2 @@
 # -*- coding: utf-8 -*-
-__version__ = '2.3.0'
+__version__ = '2.4.0'

emccd_detect/emccd_detect.py

@@ -12,7 +12,7 @@ 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
 
@@ -94,12 +94,15 @@ class EMCCDDetectBase:
         self.numel_gain_register = numel_gain_register
 
         # 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 +126,72 @@ 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
 
@@ -225,16 +264,26 @@ 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 +291,37 @@ 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)

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-2.4.0.dist-info/METADATA

@@ -0,0 +1,72 @@
+Metadata-Version: 2.1
+Name: emccd_detect
+Version: 2.4.0
+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
+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 2.4.0.  Main differences from previous version: the ability to implement readout nonlinearity and the latest version of arcticpy for charge transfer inefficiency implementation.
+
+
+## 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.dist-info → emccd_detect-2.4.0.dist-info}/RECORD

@@ -1,13 +1,13 @@
-emccd_detect/__init__.py,sha256=p-NmfUlr25lTkWkeCxbgt34N36FhFb8AqPQG7WvWx8E,45
+emccd_detect/__init__.py,sha256=FwzLqOGO--eOgOxuK6wCfzsc5yCUneMzLELAeD7Rc7Q,45
 emccd_detect/cosmics.py,sha256=wRE47QOB3fwxkH5PHTeoyLjJ0fgJki6Z8hLDPx2h3SQ,3991
-emccd_detect/emccd_detect.py,sha256=Ige6TKmeR4xHW2Jd_XOnG-NMHNodS_nr1dgGv0x6B_k,23136
-emccd_detect/nonlinearity.py,sha256=sWsYXbH5Ck2DSUntC0zbXlmsTzYw73T27tIKs41nApQ,4822
+emccd_detect/emccd_detect.py,sha256=iOLp-I6NibxJeZwmb7V5cqo5xZI3BxV5XB-1AcQLnac,26678
+emccd_detect/nonlinearity.py,sha256=DWBGjoShInMXBX0BLj6lT9dlY_lx6pdn8VU84jk_djU,4938
 emccd_detect/rand_em_gain.py,sha256=3eF9T7PNYFZT0coGZwBmNTYz6B9pj2lXxTR8ROG6_7Q,6297
 emccd_detect/util/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 emccd_detect/util/metadata.yaml,sha256=hcKTg4kMy12dfbCmmvZeKEqjeUA3BYiAcZc5vZpc3bE,1149
 emccd_detect/util/read_metadata.py,sha256=r511ENJ6zbIvLDWiVic7KsVXYrBphSdTKUQbuwocjLs,2764
 emccd_detect/util/read_metadata_wrapper.py,sha256=oBh2KpJ-uLTSIY_hPzw8sNIcJ6MENBSf38ks8OaFOSQ,5473
-emccd_detect-2.3.0.dist-info/METADATA,sha256=VDjFt5KKwFd8sM1XnF9M2DStCHWIkQ54zq6ia4P-0E8,2391
-emccd_detect-2.3.0.dist-info/WHEEL,sha256=uCRv0ZEik_232NlR4YDw4Pv3Ajt5bKvMH13NUU7hFuI,91
-emccd_detect-2.3.0.dist-info/top_level.txt,sha256=V0qxOcGf8TowSJXnTxWEMuK9BBsySwhtKNitfdokD0A,13
-emccd_detect-2.3.0.dist-info/RECORD,,
+emccd_detect-2.4.0.dist-info/METADATA,sha256=sX4JDwVH__aNVtFOAliynk1oLCiMwLSokSACT6noa9g,3039
+emccd_detect-2.4.0.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+emccd_detect-2.4.0.dist-info/top_level.txt,sha256=V0qxOcGf8TowSJXnTxWEMuK9BBsySwhtKNitfdokD0A,13
+emccd_detect-2.4.0.dist-info/RECORD,,

{emccd_detect-2.3.0.dist-info → emccd_detect-2.4.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.1.1)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

emccd_detect-2.3.0.dist-info/METADATA

@@ -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>)
-