Bumped version number

adding save_json(filename) and load_json(filename) to save and load from json
it is not recomended to save simulations as json and load them back, this process is destructive to information since json does not keep precise type information like hdf5 does, this is mostly intended as a way to just store the setup in json to simplify some ways of trading simulations around
in general json can be used in addition to hdf5 but never as a replacement

Author: Immudzen

CADET-Python.pyproj

@@ -5,13 +5,13 @@
     <SchemaVersion>2.0</SchemaVersion>
     <ProjectGuid>{12356d41-d8b4-45c3-8413-01e847dcfac2}</ProjectGuid>
     <ProjectHome />
-    <StartupFile>examples\SMB.py</StartupFile>
+    <StartupFile>examples\cadet_json.py</StartupFile>
     <SearchPath />
     <WorkingDirectory>.</WorkingDirectory>
     <OutputPath>.</OutputPath>
     <ProjectTypeGuids>{888888a0-9f3d-457c-b088-3a5042f75d52}</ProjectTypeGuids>
     <LaunchProvider>Standard Python launcher</LaunchProvider>
-    <InterpreterId>Global|ContinuumAnalytics|Anaconda37-64</InterpreterId>
+    <InterpreterId>CondaEnv|CondaEnv|cadet_devel</InterpreterId>
     <IsWindowsApplication>False</IsWindowsApplication>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)' == 'Debug'" />
@@ -29,6 +29,9 @@
     <Compile Include="cadet\__init__.py">
       <SubType>Code</SubType>
     </Compile>
+    <Compile Include="examples\cadet_json.py">
+      <SubType>Code</SubType>
+    </Compile>
     <Compile Include="examples\cadet_library.py">
       <SubType>Code</SubType>
     </Compile>
@@ -76,6 +79,7 @@
     </Compile>
   </ItemGroup>
   <ItemGroup>
+    <InterpreterReference Include="CondaEnv|CondaEnv|cadet_devel" />
     <InterpreterReference Include="Global|ContinuumAnalytics|Anaconda37-64" />
   </ItemGroup>
   <ItemGroup>

cadet/__init__.py

@@ -1,4 +1,6 @@
 name = 'CADET-python'
 
+__version__ = 0.4
+
 from .cadet import H5
 from .cadet import Cadet

cadet/cadet.py

@@ -8,6 +8,7 @@
 import subprocess
 import pprint
 import copy
+import json
 
 from pathlib import Path
 
@@ -44,6 +45,20 @@ def save(self):
         else:
             print("Filename must be set before save can be used")
 
+    def save_json(self, filename):
+        with Path(filename).open("w") as fp:
+            data = convert_from_numpy(self.root, self.transform)
+            json.dump(data, fp, indent=4, sort_keys=True)
+
+    def load_json(self, filename, update=False):
+        with Path(filename).open("r") as fp:
+            data = json.load(fp)
+            data = recursively_load_dict(data, self.inverse_transform)
+            if update:
+                self.root.update(data)
+            else:
+                self.root = data
+
     def append(self):
         "This can only be used to write new keys to the system, this is faster than having to read the data before writing it"
         if self.filename is not None:
@@ -97,6 +112,35 @@ def run(self, timeout = None, check=None):
         else:
             print("Filename must be set before run can be used")
 
+def convert_from_numpy(data, func):
+    ans = Dict()
+    for key_original,item in data.items():
+        key = func(key_original)
+        if isinstance(item, numpy.ndarray):
+            item = item.tolist()
+        
+        if isinstance(item, numpy.generic):
+            item = item.item()
+
+        if isinstance(item, bytes):
+            item = item.decode('ascii')
+        
+        if isinstance(item, Dict):
+            ans[key_original] = convert_from_numpy(item, func)
+        else:
+            ans[key] = item
+    return ans
+
+def recursively_load_dict( data, func): 
+    ans = Dict()
+    for key_original,item in data.items():
+        key = func(key_original)
+        if isinstance(item, dict):
+            ans[key] = recursively_load_dict(item, func)
+        else:
+            ans[key] = item
+    return ans
+
 def recursively_load( h5file, path, func, paths): 
     ans = Dict()
     if paths is not None:

examples/cadet_json.py

@@ -0,0 +1,9 @@
+import cadet
+
+sim = cadet.Cadet()
+sim.filename = r"C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\Example1\Dextran\dextran_pulse.h5"
+sim.load()
+
+sim.save_json(r"C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\Example1\Dextran\dextran_pulse.json")
+
+sim.load_json(r"C:\Users\kosh_000\Documents\Visual Studio 2017\Projects\CADETMatch\Examples\Example1\Dextran\dextran_pulse.json")

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="CADET",
-    version="0.3",
+    version="0.4",
     author="William Heymann",
     author_email="[email protected]",
     description="CADET is a python interface to the CADET chromatography simulator",