Changed recursively_load to correctly handle paths and their children to restrictively load only certain trees from hdf5

Author: Immudzen

.gitignore

@@ -18,3 +18,5 @@
 /ron.py
 /CADET.egg-info
 /dist
+/build/lib/cadet
+/cadet/__pycache__

CADETPython.egg-info/PKG-INFO

@@ -0,0 +1,55 @@
+Metadata-Version: 2.1
+Name: CADETPython
+Version: 0.2
+Summary: CADET is a python interface to the CADET chromatography simulator
+Home-page: https://github.com/modsim/CADET-Python
+Author: William Heymann
+Author-email: [email protected]
+License: UNKNOWN
+Description: CADET python is a file based python interface for CADET
+        CADET still must be downloaded and built from https://github.com/modsim/CADET
+        
+        CADET python almost exactly maps to the documented CADET interface except that all dataset names
+        are lowercase. This simplifies useing the interface.
+        
+        This package includes the Cadet class and H5 class. H5 can be used as a simple generic HDF5 interface.
+        
+        As an example look at setting column porosity for column 1. From the CADET manual the path for this is
+        /input/model/unit_001/COL_POROSITY
+        
+        In the python interface this becomes
+        
+        sim = Cadet()
+        sim.root.input.model.unit_001.col_porosity = 0.33
+        
+        Once the simulation has been created it must be saved before it can be run
+        
+        sim.filename = "/path/to/where/you/want/the/file.hdf5"
+        sim.save()
+        
+        #Next the path to cadet needs to be set before a simulation can be run, if running on windows you need the path to cadet-cli.exe
+        
+        sim.cadet_path = '/path/to/cadet-cli'
+        
+        #next run the simulation
+        
+        print(sim.run())
+        
+        #load the data
+        sim.load()
+        
+        
+        At this point any data can be read
+        
+        If you have a file you want to read that has already been simulated this is also easy to do
+        
+        sim = Cadet()
+        sim.filename = "/path/to/where/you/want/the/file.hdf5"
+        sim.load()
+        
+Platform: UNKNOWN
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown

CADETPython.egg-info/SOURCES.txt

@@ -0,0 +1,10 @@
+README.md
+setup.cfg
+setup.py
+CADETPython.egg-info/PKG-INFO
+CADETPython.egg-info/SOURCES.txt
+CADETPython.egg-info/dependency_links.txt
+CADETPython.egg-info/requires.txt
+CADETPython.egg-info/top_level.txt
+cadet/__init__.py
+cadet/cadet.py

CADETPython.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

CADETPython.egg-info/requires.txt

@@ -0,0 +1,3 @@
+addict
+numpy
+h5py

CADETPython.egg-info/top_level.txt

@@ -0,0 +1 @@
+cadet

cadet/cadet.py

@@ -91,24 +91,30 @@ def inverse_transform(self, x):
 
     def run(self, timeout = None, check=None):
         if self.filename is not None:
-            data = subprocess.run([self.cadet_path, self.filename], timeout = timeout, check=check, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            data = subprocess.run([self.cadet_path, self.filename], timeout = timeout, check=check, capture_output=True)
             self.return_information = data
             return data
         else:
             print("Filename must be set before run can be used")
 
 def recursively_load( h5file, path, func, paths): 
-
-    ans = {}
-    for key_original in h5file[path].keys():
-        key = func(key_original)
-        local_path = path + key
-        if paths is None or (paths is not None and local_path in paths):
+    ans = Dict()
+    if paths is not None:
+        for path in paths:
+            item = h5file[path]
+            if isinstance(item, h5py._hl.dataset.Dataset):
+                ans[path[1:]] = item[()]
+            elif isinstance(item, h5py._hl.group.Group):
+                ans[path[1:]] = recursively_load(h5file, path + '/', func, None)
+    else:
+        for key_original in h5file[path].keys():
+            key = func(key_original)
+            local_path = path + key
             item = h5file[path][key_original]
             if isinstance(item, h5py._hl.dataset.Dataset):
                 ans[key] = item[()]
             elif isinstance(item, h5py._hl.group.Group):
-                ans[key] = recursively_load(h5file, local_path + '/', func, paths)
+                ans[key] = recursively_load(h5file, local_path + '/', func, None)
     return ans 
 
 def recursively_save( h5file, path, dic, func):

examples/SMB.py

@@ -6,16 +6,17 @@
 import math
 
 from cadet import Cadet
-Cadet.cadet_path = "C:/Users/kosh_000/cadet_build/CADET-dev/MS_SMKL_RELEASE/bin/cadet-cli.exe"
+#Cadet.cadet_path = "C:/Users/kosh_000/cadet_build/CADET-dev/MS_SMKL_RELEASE/bin/cadet-cli.exe"
+Cadet.cadet_path = "C:/Users/kosh_000/cadet_build/CADET/VCPKG/bin/cadet-cli.exe"
 
 #use to render results
 import matplotlib.pyplot as plt
 
 #number of columns in a cycle
-cycle_size = 4
+cycle_size = 8
 
 #number of cycles
-cycles = 7
+cycles = 4
 
 #number of times flows have to be expanded for a 4-zone model
 repeat_size = int(cycle_size/4)
@@ -121,7 +122,7 @@ def createSimulation(simulation):
         col.ncomp = 2
         col.cross_section_area = math.pi * (0.02**2)/4.0
         col.col_dispersion = 3.8148e-20
-        col.col_length = 0.25
+        col.col_length = 0.25/repeat_size
         col.col_porosity = 0.83
         col.init_c = [0.0, 0.0]
         col.init_q = [0.0, 0.0]

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="CADET",
-    version="0.2",
+    version="0.3",
     author="William Heymann",
     author_email="[email protected]",
     description="CADET is a python interface to the CADET chromatography simulator",