Fixes for not recognizing PSF image when trying to use PointSource-ty…

…pe functions, including

keeping track of whether functions in models require PSFs.
Changed Imfit "nproc" parameter to "maxThreads".
Attempting to use version 1.9 of Imfit for libimfit.a.
Updated to version 0.12.0.

docs/conf.py

@@ -26,9 +26,9 @@
 author = 'Peter Erwin'
 
 # The short X.Y version
-version = '0.11'
+version = '0.12'
 # The full version, including alpha/beta/rc tags
-release = '0.11.2'
+release = '0.12.0'
 
 
 # -- General configuration ---------------------------------------------------

howto_new_distribution.txt

@@ -5,16 +5,18 @@ Working by default in ~/coding/pyimfit on Mac.
 
 [opt]1. Generate updated libimfit.a for macOS, IF NECESSARY
     A. [mac] cd imfit
-    B. [mac] scons --clang-openmp libimfit.a
-    C. [mac] cp libimfit.a ../prebuilt/macos
+    B. [mac] git pull origin master   [if necessary]
+    C. [mac] scons --clang-openmp libimfit.a
+    D. [mac] cp libimfit.a ../prebuilt/macos
     # copy updated Imfit C++ header files
-    D. [mac] cd .. ; ./update_from_imfit.sh
+    E. [mac] cd .. ; ./update_from_imfit.sh
 
 [opt]2. Generate updated libimfit.a for Linux [VM: ubuntu64-16_dev], IF NECESSARY
     A. [vm] cd /home/vagrant/build/pyimfit/imfit
-    B. [vm] scons libimfit.a
-    E. [vm] cp libimfit.a /vagrant/transfer
-    F. [mac] cp ~/vagrant/ubuntu64-16_dev/transfer/libimfit.a ./prebuilt/linux64
+    B. [vm] git pull origin master   [if necessary]
+    C. [vm] scons libimfit.a
+    D. [vm] cp libimfit.a /vagrant/transfer
+    E. [mac] cp ~/vagrant/ubuntu64-16_dev/transfer/libimfit.a ./prebuilt/linux64
 
 3. Do new "develop" install and run tests on macOS
     [mac] $ pip3 install -e ./

libimfit/include/count_cpu_cores.h

@@ -0,0 +1,10 @@
+// Code for determining the number of *physical* CPU cores on a computer;
+// useful for determining how many threads to use for OpenMP and (especially)
+// FFTW.
+
+#ifndef _COUNT_CPU_CORES_H_
+#define _COUNT_CPU_CORES_H_
+
+int GetPhysicalCoreCount( );
+
+#endif  // _COUNT_CPU_CORES_H_

libimfit/include/definitions.h

@@ -10,6 +10,18 @@
 #ifndef _DEFINITIONS_H_
 #define _DEFINITIONS_H_
 
+#include <string>
+#include <vector>
+#include <map>
+#include <signal.h>   // for sig_atomic_t
+
+using namespace std;
+
+#ifndef NO_SIGNALS
+// volatile sig_atomic_t  stopSignal_flag;
+extern volatile sig_atomic_t  stopSignal_flag;
+#endif
+
 
 const int  MAXLINE = 1024;
 const int MAX_FILENAME_LENGTH = 512;
@@ -23,7 +35,7 @@ const double MEMORY_WARNING_LIMT = 1073741824.0;   /* 1 gigabyte */
 // imfit-related
 #define DEFAULT_IMFIT_CONFIG_FILE   "imfit_config.dat"
 #define DEFAULT_OUTPUT_PARAMETER_FILE   "bestfit_parameters_imfit.dat"
-
+#define USER_INTERRUPT_OUTPUT_PARAMETER_FILE   "current_parameters_imfit.dat"
 
 // makeimage-related
 #define DEFAULT_MAKEIMAGE_OUTPUT_FILENAME   "modelimage.fits"
@@ -68,16 +80,22 @@ const int  MASK_ZERO_IS_BAD  =       20;  /// alternate input mask format (good
 
 
 
+/* STRING DEFINITIONS FOR PARAMETER NAMES */
+const std::string  X0_string("X0");
+const std::string  Y0_string("Y0");
+
+
+
 /* Output string formats for printing parameter values */
 #define XY_FORMAT "%s%s\t\t%.4f\n"
 #define XY_FORMAT_WITH_ERRS "%s%s\t\t%.4f # +/- %.4f\n"
 #define XY_FORMAT_WITH_LIMITS "%s%s\t\t%.4f\t\t%g,%g\n"
 #define XY_FORMAT_WITH_FIXED "%s%s\t\t%.4f\t\tfixed\n"
-#define PARAM_FORMAT "%s%s\t\t%7g\n"
-#define PARAM_FORMAT_WITH_ERRS "%s%s\t\t%7g # +/- %.5g\n"
-#define PARAM_FORMAT_WITH_LIMITS "%s%s\t\t%7g\t\t%g,%g\n"
-#define PARAM_FORMAT_WITH_FIXED "%s%s\t\t%7g\t\tfixed\n"
-
-
+// the following do *not* have "\n" at the end
+#define PARAM_FORMAT "%s%s\t\t%7g"
+#define PARAM_FORMAT_WITH_ERRS "%s%s\t\t%7g # +/- %.5g"
+#define PARAM_FORMAT_WITH_LIMITS "%s%s\t\t%7g\t\t%g,%g"
+#define PARAM_FORMAT_WITH_FIXED "%s%s\t\t%7g\t\tfixed"
+#define UNITS_FORMAT "\t%s%s"
 
 #endif /* _DEFINITIONS_H_ */

libimfit/include/function_object.h

@@ -75,7 +75,7 @@ class FunctionObject
     // override in derived classes only if said class is a "background" object
     // which should *not* be used in total flux calculations
     /// Returns true if class can calculate total flux internally
-    virtual bool IsBackground(  ) { return(false); }
+    virtual bool IsBackground(  ) { return isBackground; }
     // override in derived classes only if said class *can* calcluate total flux
     /// Returns true if class can calculate total flux internally
     virtual bool CanCalculateTotalFlux(  ) { return(false); }
@@ -95,6 +95,13 @@ class FunctionObject
     // probably no need to modify this:
     virtual void GetParameterNames( vector<string> &paramNameList );
 
+    bool HasParameterUnits( ) { return parameterUnitsExist; };
+
+    // probably no need to modify this:
+    virtual void GetParameterUnits( vector<string> &paramUnitList );
+
+    virtual void GetExtraParamsDescription( vector<string> &outputLines );
+
     // probably no need to modify this:
     virtual int GetNParams( );
 
@@ -110,8 +117,11 @@ class FunctionObject
   protected:
     int  nParams;  ///< number of input parameters that image-function uses
     bool  doSubsampling;
-    bool  extraParamsSet;
-    vector<string>  parameterLabels;
+    bool  isBackground = false;
+    bool  parameterUnitsExist = false;
+    bool  extraParamsSet = false;
+    vector<string>  parameterLabels, parameterUnits;
+    map<string, string>  inputExtraParams;
     string  functionName, shortFunctionName, label;
     double  ZP;
 

libimfit/include/model_object.h

@@ -168,6 +168,7 @@ class ModelObject
 
     virtual string GetParamHeader( );
 
+
     // common, but Specialized by ModelObject1D
     virtual int PrintModelParamsToStrings( vector<string> &stringVector, double params[], 
 									double errs[], const char *prefix="", bool printLimits=false );

libimfit/include/mpfit.h

@@ -126,6 +126,7 @@ typedef int (*mp_func)(int m, /* Number of functions (elts of fvec) */
 #define MP_FTOL (6)              /* ftol is too small; no further improvement*/
 #define MP_XTOL (7)              /* xtol is too small; no further improvement*/
 #define MP_GTOL (8)              /* gtol is too small; no further improvement*/
+#define MP_SIGINT (100)          /* PE: user typed Ctrl-C */
 
 /* Double precision numeric constants */
 #define MP_MACHEP0 2.2204460e-16

libimfit/include/oversampled_region.h

@@ -60,7 +60,8 @@ class OversampledRegion
     int  nRegionColumns, nRegionRows, nRegionVals;
     int  x1_region, y1_region;
     int  nMainImageColumns, nMainImageRows, nMainPSFColumns, nMainPSFRows;
-    int  nModelColumns, nModelRows, nModelVals;
+    int  nModelColumns, nModelRows;
+    long  nModelVals;
     bool  doConvolution, setupComplete, modelVectorAllocated;
     double  *modelVector;
     string  debugImageName;

libimfit/include/psf_interpolators.h

@@ -81,4 +81,22 @@ class PsfInterpolator_lanczos2 : public PsfInterpolator
     double *psfDataArray;
 };
 
+
+// Derived class using Lanczos3 kernel
+class PsfInterpolator_lanczos3 : public PsfInterpolator
+{
+  public:
+  PsfInterpolator_lanczos3( double *inputImage, int nCols_image, int nRows_image );
+
+  ~PsfInterpolator_lanczos3( );
+
+  double GetValue( double x, double y );
+
+  private:
+    // new data members
+    double *xArray;
+    double *yArray;
+    double *psfDataArray;
+};
+
 #endif   // _PSF_INTERPOLATORS_H_

make_upload.sh

@@ -11,6 +11,7 @@ if [[ $# -lt 1 ]]; then
 fi
 
 # Make sdist (.tar.gz) and macOS binary wheels
+python3.11 setup.py sdist bdist_wheel
 python3.10 setup.py sdist bdist_wheel
 python3.9 setup.py sdist bdist_wheel
 python3.8 setup.py bdist_wheel
@@ -19,6 +20,7 @@ python3.6 setup.py bdist_wheel
 # Copy shared libs into wheel using delocate
 VERSION_NUM=$1
 cd dist
+delocate-wheel -w fixed_wheels -v pyimfit-${VERSION_NUM}-cp311-cp311-macosx_10_9_universal2.whl
 delocate-wheel -w fixed_wheels -v pyimfit-${VERSION_NUM}-cp310-cp310-macosx_10_9_universal2.whl
 delocate-wheel -w fixed_wheels -v pyimfit-${VERSION_NUM}-cp39-cp39-macosx_10_9_x86_64.whl
 delocate-wheel -w fixed_wheels -v pyimfit-${VERSION_NUM}-cp38-cp38-macosx_10_9_x86_64.whl
@@ -35,7 +37,8 @@ then
   python3 -m twine upload --repository testpypi dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp37-cp37m-macosx_10_9_x86_64.whl
   python3 -m twine upload --repository testpypi dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp38-cp38-macosx_10_9_x86_64.whl
   python3 -m twine upload --repository testpypi dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp39-cp39-macosx_10_9_x86_64.whl
-  python3 -m twine upload --repository testpypi dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp310-cp310-macosx_10_9_x86_64.whl
+  python3 -m twine upload --repository testpypi dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp310-cp310-macosx_10_9_universal2.whl
+  python3 -m twine upload --repository testpypi dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp311-cp311-macosx_10_9_universal2.whl
   echo ""
 else
   echo "   Doing standard upload to PyPI"
@@ -45,6 +48,7 @@ else
   python3 -m twine upload dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp38-cp38-macosx_10_9_x86_64.whl
   python3 -m twine upload dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp39-cp39-macosx_10_9_x86_64.whl
   python3 -m twine upload dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp310-cp310-macosx_10_9_universal2.whl
+  python3 -m twine upload dist/fixed_wheels/pyimfit-${VERSION_NUM}-cp311-cp311-macosx_10_9_universal2.whl
   echo ""
 fi
 

new_notes_and_todo_for_python-wrapper_code.txt

@@ -6,6 +6,40 @@ PLAN:
     Imfit.fit and Imfit.doFit
 
 
+[ ] Rewrite SimpleModelDescription from scratch
+    -- this class is currently a mess
+    -- should just be a light wrapper around ModelDescription, with as little as possible
+    separate/unique code
+
+[ ] Fix bug in trying to use PointSource-type (PSF interpolation) functios
+	[X] I. Modify ModelObjectWrapper.__init__() to accept optional PSF & normalization flag
+
+		If PSF and flag are non-None, ModelObjectWrapper.__init__() should call setPSF()
+		*before* calling ModelObjectWrapper._addFunctions()
+
+	[X] II. Move code from ModelObjectWrapper.setPSF() into ModelObjectWrapper.__init__();
+	delete ModelObjectWrapper.setPSF()
+
+	[X] III. Modify Imfit._setupModel() so that it initializes ModelObjectWrapper with
+	new interface, including PSF.
+		np.asarray(self._psf), self._normalizePSF
+
+	[X] IV. Modify Imfit._setupModel() to remove call to self._modelObjectWrapper.setPSF()
+
+    [X] Run pytest test_imfit.py to see if test passes
+
+    [ ] Modify ModelDescription to include reporting if it contains PointSource-type functions
+        -- attribute hasPointSources [bool]
+        [ ] Add tests to test_descriptions.py
+        [ ] Write code to pass tests
+
+    [ ] Add error-checking to catch and report if we try to instantiate Imfit object when
+    model has PointSource and we didn't supply one (raise TypeError)
+        [ ] Write test (in test_imfit.py) to check this
+
+        [ ] Write code in Imfit.__init__ to make test pass
+
+
 [ ] Modify various methods in Imfit class to check whether _modelObjectWrapper has been
     instantiated or not.
 

notes_on_bugs_and_improvements.txt

@@ -1,3 +1,29 @@
+* Problems with missing symbols when importing pyimfit into Python session:
+
+In trying to use the updated version of PyImfit (v0.12, based on Imfit v1.9),
+I encountered the following when trying to import pyimfit into a Python
+session:
+
+Traceback (most recent call last):
+  File "<stdin>", line 1, in <module>
+  File "/Users/erwin/coding/pyimfit/pyimfit/__init__.py", line 4, in <module>
+    from .pyimfit_lib import convolve_image, make_imfit_function, ModelObjectWrapper  # type: ignore
+ImportError: dlopen(/Users/erwin/coding/pyimfit/pyimfit/pyimfit_lib.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace (__Z20GetPhysicalCoreCountv)
+
+The missing symbol is a mangled form of GetPhysicalCoreCount, which is in the new (in v1.9)
+count_cpu_cores.cpp code in Imfit. Since convolver.cpp uses that function, it needs to be
+in the library (libimfit.a) file.
+
+The problem turned out to be that the compiled object code for that file -- count_cpu_cores.o --
+was *not* in the list of object files to be incorporated into libimfit.a inside SConstruct.
+Modifying the base_for_lib_objstring string in SConstruct to add "count_cpu_cores" fixed the problem.
+
+(Note that the SConstruct file in the current Imfit repo already had that modification, but
+the Github version and the version inside the pyimfit directory did *not*; this has been
+fixed.)
+
+
+
 * Problem with attribute access:
 
 Problem encountered in writing unit tests for read_function_set()

pyimfit/__init__.py

@@ -14,4 +14,4 @@
 imageFunctionList = get_function_list()
 imageFunctionDict = get_function_dict()
 
-__version__ = "0.11.2"
+__version__ = "0.12.0"