Feature/post processing

.gitattributes

@@ -0,0 +1,2 @@
+*.raw filter=lfs diff=lfs merge=lfs -text
+*.hdf5 filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -1,5 +1,3 @@
-*.raw
-*.hdf5
 *.dat
 *.egg
 *.egg-info/
@@ -11,3 +9,6 @@
 .DS_Store
 .vscode/settings.json
 build/
+venv
+.idea
+

doc/users/pymepixacq.rst

@@ -5,32 +5,27 @@ PymepixAcq - Command line
 ===========================
 
 
-Included with pymepix is a command line code using the pymepix library to acquire from timepix. It is run using::
-
-    pymepix-acq --time 10 --output my_file
+Included with pymepix is a command line code using the pymepix library to acquire from timepix. The command line interface includes two different commands:
+ - "connect": to connect to a running timepix camera and record data
+ - "post-process": to post-process recorded raw data files into easier usable hdf5 files containing raw and centroided data
 
 Doing::
 
     pymepix-acq --help
 
-
 Outputs the help::
 
-    usage: pymepix-acq [-h] [-i IP] [-p PORT] [-s SPX] [-v BIAS] -t TIME -o OUTPUT
-                    [-d DECODE] [-T TOF]
+    usage: pymepix-acq [-h] {connect,post-process} ...
 
     Timepix acquisition script
 
+    positional arguments:
+        {connect,post-process}
+         connect             Connect to TimePix camera and acquire data.
+         post-process        Perform post-processing for an acquired raw data file.
+
     optional arguments:
-    -h, --help                 show this help message and exit
-    -i IP, --ip IP             IP address of Timepix
-    -p PORT, --port PORT       TCP port to use for the connection
-    -s SPX, --spx SPX          Sophy config file to load
-    -v BIAS, --bias BIAS       Bias voltage in Volts
-    -t TIME, --time TIME       Acquisition time in seconds
-    -o OUTPUT, --output OUTPUT output filename prefix
-    -d DECODE, --decode DECODE Store decoded values instead
-    -T TOF, --tof TOF          Compute TOF if decode is enabled
-
-
-TODO: MORE DOCS
+        -h, --help            show this help message and exit
+
+
+You can access the documentation for both commands by executing "pymepix-acq connect -h" or "pymepix-acq post-process -h" respectively.

pymepix/__init__.py

@@ -19,5 +19,6 @@
 # see <https://www.gnu.org/licenses/>.
 
 from pymepix.processing import MessageType
-from pymepix.pymepix import PollBufferEmpty, Pymepix
+from pymepix.pymepix_connection import PollBufferEmpty, PymepixConnection
 from pymepix.timepixdef import *
+from pymepix.post_processing import run_post_processing

pymepix/core/log.py

@@ -19,13 +19,12 @@
 # see <https://www.gnu.org/licenses/>.
 
 
+from abc import abstractmethod
 import logging
-import threading
-from multiprocessing import Queue
+import multiprocessing as mp
 
 __all__ = ["Logger", "ProcessLogger"]
 
-
 class PymepixLogger(object):
     """Base class for logging in pymepix
 
@@ -41,91 +40,19 @@ class PymepixLogger(object):
 
     """
 
-    _proc_log_queue = Queue()
-
-    _init = False
-
-    @classmethod
-    def getLogQueue(cls):
-        """Provides logging queue for multiprocessing logging
-
-        Returns
-        --------
-        :obj:`multiprocessing.Queue`
-            Queue where logs should go
-
-        """
-        return cls._proc_log_queue
-
-    @classmethod
-    def _logging_thread(cls):
-        """This thread collects logs from Processes and writes them to stream"""
-
-        thread_log = PymepixLogger.getLogger("log_thread")
-        log_queue = cls.getLogQueue()
-
-        thread_log.info("Starting Multiprocess logging")
-        while True:
-            name, log_level, message, args, kwargs = log_queue.get()
-            _log = logging.getLogger(name)
-            _log.log(log_level, message, *args, **kwargs)
-
-    @classmethod
-    def getRootLogger(cls):
-        return cls._root_logger
-
-    @classmethod
-    def getLogger(cls, name):
-        return logging.getLogger("pymepix.{}".format(name))
-
-    @classmethod
-    def reInit(cls):
-        if cls._init is False:
-            cls._root_logger = logging.getLogger("pymepix")
-
-            cls._root_logger.info("Reinitializing PymepixLogger")
-            cls._log_thread = threading.Thread(target=cls._logging_thread)
-            cls._log_thread.daemon = True
-            cls._log_thread.start()
-        cls._init = True
+
 
     def __init__(self, name):
+        self._logger = self.getLogger(name)
         self._log_name = "pymepix.{}".format(name)
-        PymepixLogger.reInit()
 
     @property
     def logName(self):
         return self._log_name
 
-    def info(self, message, *args, **kwargs):
-        pass
-
-    def warning(self, message, *args, **kwargs):
-        pass
-
-    def debug(self, message, *args, **kwargs):
-        pass
-
-    def error(self, message, *args, **kwargs):
-        pass
-
-    def critical(self, message, *args, **kwargs):
-        pass
-
-
-class Logger(PymepixLogger):
-    """Standard logging using logger library
-
-    Parameters
-    -----------
-    name : str
-        Name used for logging
-
-    """
-
-    def __init__(self, name):
-        PymepixLogger.__init__(self, name)
-        self._logger = logging.getLogger(self.logName)
+    @abstractmethod
+    def getLogger(cls, name):
+        pass 
 
     def info(self, message, *args, **kwargs):
         """ See :class:`logging.Logger` """
@@ -148,8 +75,8 @@ def critical(self, message, *args, **kwargs):
         self._logger.critical(message, *args, **kwargs)
 
 
-class ProcessLogger(PymepixLogger):
-    """Sends logs to queue to be processed by logging thread
+class Logger(PymepixLogger):
+    """Standard logging using logger library
 
     Parameters
     -----------
@@ -161,27 +88,22 @@ class ProcessLogger(PymepixLogger):
     def __init__(self, name):
         PymepixLogger.__init__(self, name)
         self._logger = logging.getLogger(self.logName)
-        self._log_queue = PymepixLogger.getLogQueue()
 
-    def info(self, message, *args, **kwargs):
-        """ See :class:`logging.Logger` """
-        self._log_queue.put((self._log_name, logging.INFO, message, args, kwargs))
+    def getLogger(cls, name):
+        return logging.getLogger("pymepix.{}".format(name))
 
-    def warning(self, message, *args, **kwargs):
-        """ See :class:`logging.Logger` """
-        self._log_queue.put((self._log_name, logging.WARNING, message, args, kwargs))
 
-    def debug(self, message, *args, **kwargs):
-        """ See :class:`logging.Logger` """
-        self._log_queue.put((self._log_name, logging.DEBUG, message, args, kwargs))
+class ProcessLogger(PymepixLogger):
+    """Sends logs to queue to be processed by logging thread
 
-    def error(self, message, *args, **kwargs):
-        """ See :class:`logging.Logger` """
-        self._log_queue.put((self._log_name, logging.ERROR, message, args, kwargs))
+    Parameters
+    -----------
+    name : str
+        Name used for logging
 
-    def critical(self, message, *args, **kwargs):
-        """ See :class:`logging.Logger` """
-        self._log_queue.put((self._log_name, logging.CRITICAL, message, args, kwargs))
+    """
+    def getLogger(self, name):
+        return mp.get_logger()
 
 
 def main():