updates to pyprismatic to allow for building with HDF5 libraries; cor…

…rected input mappings; fixed unit errors in inputs and added input parser to prevent invalid input combinations

pyprismatic/__init__.py

@@ -15,6 +15,19 @@
 from . import fileio  # noqa
 from pyprismatic.params import Metadata
 
+def keySearch(dictionary,layer):
+    layer+=1
+    try:
+        keys = dictionary.keys()
+        for key in keys:
+            printStr = ""
+            for i in range(0,layer):
+                printStr += "--"
+            printStr += key
+            print(printStr)
+            keySearch(dictionary[key],layer)
+    except:
+        a = 1
 
 def demo():
     import os
@@ -33,15 +46,16 @@ def demo():
 14  4.0725  4.0725  4.0725  1.0  0.076\n\
 -1"
         )
-    meta = Metadata(filenameAtoms="temp.XYZ", filenameOutput="output.mrc")
+    meta = Metadata(filenameAtoms="temp.XYZ", filenameOutput="demo.h5")
     meta.algorithm = "multislice"
     meta.go()
     import numpy as np
-    from pyprismatic.fileio import readMRC
-    import matplotlib.pyplot as plt
+    #from pyprismatic.fileio import readMRC
+    import h5py
+    #result = readMRC("output.mrc")
+
+    demoFile = h5py.File('demo.h5','r')
+    print('demo.h5 filestructure:')
+    keySearch(demoFile,0)
 
-    result = readMRC("output.mrc")
-    plt.figure()
-    plt.imshow(np.squeeze(np.sum(result, axis=2)))
-    plt.show()
     os.remove("temp.XYZ")

pyprismatic/core.cpp

@@ -16,6 +16,8 @@
 #include "configure.h"
 #include "parseInput.h"
 #include "go.h"
+#include <iostream>
+#include <stdio.h>
 #ifdef PRISMATIC_ENABLE_GPU
 #include "cuprismatic.h"
 #endif //PRISMATIC_ENABLE_GPU
@@ -45,7 +47,7 @@ static PyObject *pyprismatic_core_go(PyObject *self, PyObject *args)
 #endif //PRISMATIC_ENABLE_GPU
 
 	if (!PyArg_ParseTuple(
-			args, "iissdddiddddiiiddiiiiiddddddddddddddispppppddsiiiddddd",
+			args, "iissdddiddddiiiddiiiiiddddddddddddddispppppddsiiiiddddd",
 			&interpolationFactorX,
 			&interpolationFactorY,
 			&filenameAtoms,
@@ -94,6 +96,7 @@ static PyObject *pyprismatic_core_go(PyObject *self, PyObject *args)
 			&transferMode,
 			&saveDPC_CoM,
 			&savePotentialSlices,
+			&nyquistSampling,
 			&numSlices,
 			&zStart,
 			&scanWindowXMin_r,
@@ -120,8 +123,8 @@ static PyObject *pyprismatic_core_go(PyObject *self, PyObject *args)
 	meta.tileX = tileX;
 	meta.tileY = tileY;
 	meta.tileZ = tileZ;
-	meta.E0 = E0;
-	meta.alphaBeamMax = alphaBeamMax;
+	meta.E0 = E0 * 1000;
+	meta.alphaBeamMax = alphaBeamMax / 1000;
 	meta.numGPUs = numGPUs;
 	meta.numStreamsPerGPU = numStreamsPerGPU;
 	meta.numThreads = numThreads;
@@ -133,10 +136,10 @@ static PyObject *pyprismatic_core_go(PyObject *self, PyObject *args)
 	meta.probeDefocus = probeDefocus;
 	meta.C3 = C3;
 	meta.C5 = C5;
-	meta.probeSemiangle = probeSemiangle;
-	meta.detectorAngleStep = detectorAngleStep;
-	meta.probeXtilt = probeXtilt;
-	meta.probeYtilt = probeYtilt;
+	meta.probeSemiangle = probeSemiangle /1000;
+	meta.detectorAngleStep = detectorAngleStep /1000;
+	meta.probeXtilt = probeXtilt /1000;
+	meta.probeYtilt = probeYtilt /1000;
 	meta.scanWindowXMin = scanWindowXMin;
 	meta.scanWindowXMax = scanWindowXMax;
 	meta.scanWindowYMin = scanWindowYMin;
@@ -161,8 +164,8 @@ static PyObject *pyprismatic_core_go(PyObject *self, PyObject *args)
 	meta.save4DOutput = save4DOutput;
 	meta.savePotentialSlices = savePotentialSlices;
 	meta.saveDPC_CoM = saveDPC_CoM;
-	meta.integrationAngleMin = integrationAngleMin;
-	meta.integrationAngleMax = integrationAngleMax;
+	meta.integrationAngleMin = integrationAngleMin / 1000;
+	meta.integrationAngleMax = integrationAngleMax / 1000;
 	meta.nyquistSampling = nyquistSampling;
 
 	if (std::string(transferMode) == "singlexfer")
@@ -179,12 +182,19 @@ static PyObject *pyprismatic_core_go(PyObject *self, PyObject *args)
 	}
 
 	// print metadata
-	meta.toString();
+	//meta.toString();
+	int scratch = Prismatic::writeParamFile(meta,"scratch_param.txt");
 
-	Prismatic::go(meta);
+	Prismatic::Metadata<PRISMATIC_FLOAT_PRECISION> tmp_meta;
+	if(Prismatic::parseParamFile(tmp_meta,"scratch_param.txt")) 
+	{
+		Prismatic::go(meta);
+	}else{
+		std::cout << "Invalid parameters detected. Cancelling calculation, please check inputs." << std::endl;
+	}
 	// configure simulation behavior
 	//	Prismatic::configure(meta);
-
+	//std::remove("scratch_param.txt");
 	// execute simulation
 	//	Prismatic::execute_plan(meta);
 

pyprismatic/params.py

@@ -84,8 +84,6 @@ class Metadata:
         "potBound",
         "numFP",
         "sliceThickness",
-        "numSlices",
-        "zStart",
         "cellDimX",
         "cellDimY",
         "cellDimZ",
@@ -113,23 +111,25 @@ class Metadata:
         "scanWindowXMax",
         "scanWindowYMin",
         "scanWindowYMax",
-        "scanWindowXMin_r",
-        "scanWindowXMax_r",
-        "scanWindowYMin_r",
-        "scanWindowYMax_r",
         "randomSeed",
         "algorithm",
         "includeThermalEffects",
         "alsoDoCPUWork",
         "save2DOutput",
         "save3DOutput",
         "save4DOutput",
-        "saveDPC_CoM",
-        "savePotentialSlices",
-        "nyquistSampling",
         "integrationAngleMin",
         "integrationAngleMax",
         "transferMode",
+        "saveDPC_CoM",
+        "savePotentialSlices",
+        "nyquistSampling",
+        "numSlices",
+        "zStart",
+        "scanWindowXMin_r",
+        "scanWindowXMax_r",
+        "scanWindowYMin_r",
+        "scanWindowYMax_r",
     ]
 
     str_fields: List[str] = ["algorithm", "transferMode"]
@@ -140,7 +140,8 @@ class Metadata:
         "tileX",
         "tileY",
         "tileZ",
-        "numFP" "numGPUs",
+        "numFP",
+        "numGPUs",
         "numStreamsPerGPU",
         "numThreads",
         "batchSizeTargetCPU",
@@ -241,7 +242,7 @@ def __init__(self, *args, **kwargs):
         self.save2DOutput = False
         self.save3DOutput = True
         self.save4DOutput = False
-        self.saveDPC_COM = False
+        self.saveDPC_CoM = False
         self.savePotentialSlices = False
         self.nyquistSampling = False
         self.integrationAngleMin = 0

requirements.txt

@@ -1,2 +1,3 @@
 numpy>=1.13.0
 matplotlib>=2.0.2
+h5py>=2.9.0

setup.py

@@ -13,9 +13,13 @@
 
 from setuptools import setup, Extension
 from setuptools.command.install import install
+from setuptools.command.develop import develop
 import sys
 import os
 
+#os.environ['CC'] = 'gcc-7'
+#os.environ['CXX'] = 'g++-7'
+
 prismatic_extra_definitions = []
 prismatic_libs = []
 
@@ -24,7 +28,16 @@
 # the shared library (along with CUDA files) are the "extra" sources and in CPU-mode they are added to the Python package sources.
 # The reason for doing it this way is for user convenience so that compiling/linking to an extra Prismatic library is not required until
 # enabling for GPU, at which point it is already necessary for the other CUDA libraries.
+
 prismatic_sources_base = ["pyprismatic/core.cpp"]
+obj_prefix = "build/CMakeFiles/prismatic.dir/src/"
+prismatic_gpu_objects = ["prismatic_generated_Multislice_calcOutput.cu.o",
+    "prismatic_generated_PRISM02_calcSMatrix.cu.o",
+    "prismatic_generated_PRISM03_calcOutput.cu.o",
+    "prismatic_generated_utility.cu.o",
+    ]
+
+prismatic_gpu_objects = [obj_prefix + obj for obj in prismatic_gpu_objects]
 prismatic_sources_extra = [
     "src/go.cpp",
     "src/atom.cpp",
@@ -40,17 +53,18 @@
     "src/utility.cpp",  #
     "src/WorkDispatcher.cpp",
 ]
+
 prismatic_sources = prismatic_sources_base
 prismatic_include_dirs = ["./include"]
 prismatic_library_dirs = []
+prismatic_extra_objects = [] #"/usr/local/hdf/lib/libhdf5_hl.so","/usr/local/hdf/lib/libhdf5.so","/usr/local/hdf/lib/libhdf5_hl_cpp.so","/usr/local/hdf/lib/libhdf5_cpp.so"]
 
 if os.name == "nt":  # check for Windows OS
     prismatic_libs = ["libfftw3f-3"]
 else:
-    prismatic_libs = ["fftw3f", "fftw3f_threads"]
+    prismatic_libs = ["fftw3f", "fftw3f_threads","hdf5_hl","hdf5","hdf5_hl_cpp","hdf5_cpp","pthread","dl","m"]
 prismatic_extra_compile_defs = ["-std=c++11"]
 
-
 class InstallCommand(install):
     user_options = install.user_options + [("enable-gpu", None, None)]
 
@@ -64,14 +78,28 @@ def finalize_options(self):
     def run(self):
         install.run(self)
 
+class DevelopCommand(develop):
+    user_options = develop.user_options + [("enable-gpu", None, None)]
+
+    def initialize_options(self):
+        develop.initialize_options(self)
+        self.enable_gpu = False
+
+    def finalize_options(self):
+        develop.finalize_options(self)
+
+    def run(self):
+        develop.run(self)
 
 if (
     "--enable-gpu" in sys.argv
 ):  # GPU-mode, add some macro definitions and link with the CUDA libraries
     prismatic_extra_definitions.extend(
         [("PRISMATIC_ENABLE_GPU", 1), ("BUILDING_CUPRISMATIC", 1)]
     )
-    prismatic_libs.extend(["cuprismatic", "cufft", "cudart"])
+    prismatic_libs.extend(["cufft", "cudart"])
+    prismatic_sources.extend(prismatic_sources_extra)
+    prismatic_extra_objects.extend(prismatic_gpu_objects)
 else:  # CPU-only mode, add the extra C++ sources to the python package
     prismatic_sources.extend(prismatic_sources_extra)
 
@@ -83,16 +111,18 @@ def run(self):
     define_macros=prismatic_extra_definitions,
     library_dirs=prismatic_library_dirs,
     libraries=prismatic_libs,
+    extra_objects=prismatic_extra_objects,
 )
 
 setup(
     name="PyPrismatic",
     author="Alan (AJ) Pryor, Jr.",
     author_email="apryor6@gmail.com",
-    version="1.1.16",
+    version="1.2.0",
     description="Python wrapper for Prismatic package for fast image simulation using the PRISM and multislice algorithms in Scanning Transmission Electron Microscopy (STEM)",
     ext_modules=[pyprimsatic_core],
     packages=["pyprismatic"],
-    install_requires=["numpy>=1.13.0", "matplotlib>=2.0.2"],
-    cmdclass={"install": InstallCommand},
+    install_requires=["numpy>=1.13.0", "matplotlib>=2.0.2","h5py>=2.9.0"],
+    cmdclass={"install": InstallCommand,
+    "develop":DevelopCommand},
 )