Convert vdswrapperpart to use direct call rather than subprocess

malcolm/modules/excalibur/parts/vdswrapperpart.py

@@ -1,17 +1,14 @@
 import os
-import sys
-from subprocess import check_call
 
-#sys.path.insert(0, "/dls_sw/work/tools/RHEL6-x86_64/odin/venv/lib/python2.7/"
-#                   "site-packages")
-import h5py as h5
 import numpy as np
+import h5py as h5
+from vdsgen import SubFrameVDSGenerator
+
 from malcolm.modules.scanning.controllers import RunnableController
 from malcolm.core import method_takes, REQUIRED, Part
 from malcolm.modules.ADCore.infos import DatasetProducedInfo
 from malcolm.modules.builtin.vmetas import StringMeta, NumberMeta
 from malcolm.modules.scanpointgenerator.vmetas import PointGeneratorMeta
-from copy import deepcopy
 
 # Number of points too look ahead of the current id index to account for dropped frames
 NUM_LOOKAHEAD = 100
@@ -23,23 +20,6 @@
     "stripeWidth", NumberMeta("int16", "Width of stripes"), REQUIRED)
 class VDSWrapperPart(Part):
 
-    # Constants for vds-gen CLI app
-    #VENV = "/dls_sw/work/tools/RHEL6-x86_64/odin/venv/bin/python"
-    #VDS_GEN = "/dls_sw/work/tools/RHEL6-x86_64/odin/vds-gen/vdsgen/app.py"
-    VDS_GEN = "/dls_sw/prod/tools/RHEL6-x86_64/defaults/bin/dls-vds-gen.py"
-    EMPTY = "-e"
-    OUTPUT = "-o"
-    FILES = "-f"
-    SHAPE = "--shape"
-    DATA_TYPE = "--data_type"
-    DATA_PATH = "-d"
-    STRIPE_SPACING = "-s"
-    MODULE_SPACING = "-m"
-    FILL_VALUE = "-F"
-    SOURCE_NODE = "--source_node"
-    TARGET_NODE = "--target_node"
-    LOG_LEVEL = "-l"
-
     # Constants for class
     RAW_FILE_TEMPLATE = "FEM{}"
     OUTPUT_FILE = "EXCALIBUR"
@@ -85,7 +65,6 @@ def close_files(self):
         self.raw_datasets = []
         self.vds = None
 
-
     def _create_dataset_infos(self, generator, filename):
         uniqueid_path = "/entry/NDAttributes/NDArrayUniqueId"
         data_path = "/entry/detector/detector"
@@ -152,30 +131,28 @@ def configure(self, context, completed_steps, steps_to_do, part_info,
             self.vds.create_dataset(self.ID, initial_shape,
                                     maxshape=max_shape, dtype="int32")
             self.vds.create_dataset(self.SUM, initial_shape,
-                                    maxshape=max_shape, dtype="float64", fillvalue=np.nan)
+                                    maxshape=max_shape, dtype="float64",
+                                    fillvalue=np.nan)
         files = [params.fileTemplate % self.RAW_FILE_TEMPLATE.format(fem)
                  for fem in self.fems]
         shape = [str(d) for d in params.generator.shape] + \
                 [str(self.stripe_height), str(self.stripe_width)]
-        # Base arguments
-        #command = [self.VENV, self.VDS_GEN, params.fileDir]
-        command = [self.VDS_GEN, params.fileDir]
-        # Define empty and required arguments to do so
-        command += [self.EMPTY,
-                    self.FILES] + files + \
-                   [self.SHAPE] + shape + \
-                   [self.DATA_TYPE, self.data_type]
-        # Override default spacing and data path
-        command += [self.STRIPE_SPACING, "0",
-                    self.MODULE_SPACING, "121",
-                    self.FILL_VALUE, str(params.fillValue),
-                    self.SOURCE_NODE, "/entry/detector/detector",
-                    self.TARGET_NODE, "/entry/detector/detector"]
-        # Define output file path
-        command += [self.OUTPUT, params.fileTemplate % self.OUTPUT_FILE]
-        command += [self.LOG_LEVEL, "1"] # str(self.log.level / 10)]
-        self.log.info("VDSGen Command: %s", command)
-        check_call(command)
+
+        # Create the VDS using vdsgen
+        fgen = SubFrameVDSGenerator(
+            params.fileDir,
+            prefix=None,
+            files=files,
+            output=params.fileTemplate % self.OUTPUT_FILE,
+            source=dict(shape=shape, dtype=self.data_type),
+            source_node="/entry/detector/detector",
+            target_node="/entry/detector/detector",
+            stripe_spacing=0,
+            module_spacing=121,
+            fill_value=params.fillValue,
+            log_level=1 # DEBUG
+        )
+        fgen.generate_vds()
 
         # Store required attributes
         self.raw_paths = [os.path.abspath(os.path.join(params.fileDir, file_))

requirements/test.txt

@@ -9,5 +9,5 @@ plop==0.3.0
 pytest>=3
 pytest-catchlog
 pytest-cov
-git+https://github.com/aaron-parsons/h5py.git#egg=h5py
-git+https://github.com/dls-controls/vds-gen.git#egg=vds-gen
+h5py==2.7.1
+git+https://github.com/dls-controls/vds-gen.git@0-2#egg=vds-gen

setup.py

@@ -72,7 +72,8 @@ def add_multiversion_require(module):
     install_requires=install_requires,
     extras_require={
         'websocket':  ['tornado'],
-        'ca': ['cothread']
+        'ca': ['cothread'],
+        'hdf5': ['h5py', 'vds-gen'],
     },
     include_package_data=True,
     test_suite='nose.collector',