wip

apps/grond

@@ -24,7 +24,7 @@ def d2u(d):
 
 
 subcommand_descriptions = {
-    'init': 'print example configuration',
+    'init': 'create project structure or print example configuration',
     'events': 'print available event names for given configuration',
     'check': 'check data and configuration',
     'go': 'run Grond optimization',
@@ -35,7 +35,7 @@ subcommand_descriptions = {
 }
 
 subcommand_usages = {
-    'init': 'init [options]',
+    'init': 'init [options] <project_dir>',
     'events': 'events <configfile>',
     'check': 'check <configfile> <eventnames> ... [options]',
     'go': 'go <configfile> <eventnames> ... [options]',
@@ -145,10 +145,20 @@ def command_init(args):
 
     parser, options, args = cl_parse('init', args, setup)
 
-    dir_struct = ['gf_store']
+    project_dir = None
+    if len(args) == 1:
+        project_dir = op.join(op.curdir, args[0])
+        if op.exists(project_dir):
+            raise EnvironmentError('Directory %s already exists' % args[0])
+
+    sub_dirs = ['gf_store']
+    empty_files = []
 
     if options.waveform and not options.static:
-        dir_struct += ['data']
+        config_type = 'waveform'
+
+        sub_dirs += ['data']
+        empty_files += ['stations.xml']
         dataset_config = grond.DatasetConfig(
             stations_path='stations.txt',
             events_path='events.txt',
@@ -188,7 +198,9 @@ def command_init(args):
             )
 
     elif options.static:
-        dir_struct += ['scenes']
+        config_type = 'static'
+
+        sub_dirs += ['scenes']
         dataset_config = grond.DatasetConfig(
             events_path='events.txt',
             kite_scene_paths=['scenes'],
@@ -236,22 +248,26 @@ depth = 8000
 region = Myanmar
 --------------------------------------------'''
 
-    def create_struct(dirname):
+    if project_dir is not None:
+        logger.info('Creating empty %s project in folder %s'
+                    % (config_type, args[0]))
 
         def p(fn):
-            op.abspath(op.join(dirname, fn))
+            return op.join(project_dir, fn)
 
-        os.mkdir(op.abspath(dirname))
+        os.mkdir(op.abspath(project_dir))
+        for d in sub_dirs:
+            os.mkdir(p(d))
 
         with open(p('config.yml'), 'w') as cf:
             cf.write(str(config))
         with open(p('events.txt'), 'w') as ef:
             ef.write(events)
-        open('stations.txt', 'a').close()
-        for d in dir_struct:
-            os.mkdir(p(d))
 
-    print config
+        for fn in empty_files:
+            open(p(fn), 'w').close()
+    else:
+        print config
 
 
 def command_events(args):

src/baraddur/__init__.py

+from .server import  # noqa
\ No newline at end of file

src/baraddur/server.py

 import tornado.ioloop
 import grond
+import os
 import os.path as op
 import logging
 import numpy as num
@@ -45,6 +46,67 @@ class BaraddurBokehHandler(BokehHandler):
         self.config = config
 
 
+class GrondBokehModel(object):
+    def __init__(self, config):
+        self.config = config
+        self.set_rundir(self.config.rundir)
+
+    def set_rundir(self, rundir):
+        logger.debug('Loading problem from %s' % rundir)
+        self.rundir = rundir
+        self.problem = grond.core.load_problem_info(self.rundir)
+        self.parameters = self.problem.parameters
+        self.nparameters = self.problem.nparameters
+        self.ntargets = self.problem.ntargets
+
+    def get_models(self, skip_nmodels=0):
+        fn = op.join(self.rundir, 'models')
+        with open(fn, 'r') as f:
+            nmodels = os.fstat(f.fileno()).st_size / (self.nparameters * 8)
+            nmodels -= skip_nmodels
+            f.seek(skip_nmodels * self.nparameters * 8)
+            data = num.fromfile(
+                f, dtype='<f8', count=nmodels * self.nparameters)\
+                .astype(num.float)
+
+        nmodels = data.size/self.nparameters - skip_nmodels
+        models = data.reshape((nmodels, self.nparameters))
+
+        mods_dict = {}
+        for ip, par in enumerate(self.parameters):
+            mods_dict[par.name] = models[:, ip]
+        mods_dict['niter'] = num.arange(nmodels, dtype=num.int) + (nmodels+1)
+        return nmodels, mods_dict
+
+    def get_misfits(self, skip_nmodels=0):
+        fn = op.join(self.rundir, 'misfits')
+
+        with open(fn, 'r') as f:
+            nmodels = os.fstat(f.fileno()).st_size / (self.nparameters * 8)
+            nmodels -= skip_nmodels
+            f.seek(skip_nmodels * self.ntargets * 2 * 8)
+            data = num.fromfile(
+                f, dtype='<f8', count=nmodels*self.ntargets*2)\
+                .astype(num.float)
+
+        data = data.reshape((nmodels, self.ntargets*2))
+
+        combi = num.empty_like(data)
+        combi[:, 0::2] = data[:, :self.ntargets]
+        combi[:, 1::2] = data[:, self.ntargets:]
+
+        assert(data.size/self.nparameters - skip_nmodels == nmodels)
+        misfits = combi.reshape((nmodels, self.ntargets, 2))
+
+        mf_dict = {}
+        for it in xrange(self.ntargets):
+            mf_dict['target_%03d' % it] = misfits[:, it, 0]
+        mf_dict['target_mean'] = num.mean(misfits[:, :, 0])
+
+        mf_dict['niter'] = num.arange(nmodels, dtype=num.int) + (nmodels+1)
+        return nmodels, misfits
+
+
 class Status(BaraddurRequestHandler):
 
     class MisfitsPlot(BaraddurBokehHandler):
@@ -52,8 +114,8 @@ class Status(BaraddurRequestHandler):
         def modify_document(self, doc):
             self.nmodels = 0
             self.source = ColumnDataSource(
-                data={'n': [],
-                      'gm': []})
+                data={'n': num.ndarray(0),
+                      'gm': num.ndarray(0)})
             self.update_misfits()
 
             plot = figure(webgl=True,
@@ -101,7 +163,7 @@ class Parameters(BaraddurRequestHandler):
 
             self.source = ColumnDataSource()
             for p in ['n'] + [p.name for p in problem.parameters]:
-                self.source.add([], p)
+                self.source.add(num.ndarray(0), p)
             self.update_parameters()
 
             plots = []
@@ -231,7 +293,7 @@ class BaraddurConfig(Object):
         String.T(),
         default=['*'],
         optional=True,
-        help='List of allowed hosts.')
+        help='List of allowed hosts, default is all \'*\'.')
     port = Int.T(
         default=8080,
         optional=True,

src/problems.py

@@ -126,7 +126,7 @@ class Problem(Object):
         guts.dump(self, filename=fn)
 
     def dump_problem_data(self, dirname, x, ms, ns):
-        fn = op.join(dirname, 'x')
+        fn = op.join(dirname, 'models')
         if not isinstance(x, num.ndarray):
             x = num.array(x)
         with open(fn, 'ab') as f: