JorgeVB/code_unlearning_dataset · Datasets at Hugging Face

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Handling of Exceptions. Parameters ---------- exc : list, tuple Information of the exception of the format (type, value, traceback). Uses the return value of sys.exc_info(). def handle_err(self, exc): '''Handling of Exceptions. Parameters ------...
Returns the configuration for a given module ID. The working directory is searched for a file matching the module_id with the given run number. If no run number is defined the last successfull run defines the run number. def get_configuration(self, module_id, run_number=None): ''' Retu...
Select module and give access to the module. def select_module(self, module_id): ''' Select module and give access to the module. ''' if not isinstance(module_id, basestring) and isinstance(module_id, Iterable) and set(module_id) - set(self._modules): raise ValueError('Module IDs in...
Deselect module and cleanup. def deselect_module(self): ''' Deselect module and cleanup. ''' self._enabled_fe_channels = [] # ignore any RX sync errors self._readout_fifos = [] self._filter = [] self._converter = [] self.dut['TX']['OUTPUT_ENABLE'] = 0 se...
Waiting for all threads to appear, then continue. def enter_sync(self): ''' Waiting for all threads to appear, then continue. ''' if self._scan_threads and self.current_module_handle not in [t.name for t in self._scan_threads]: raise RuntimeError('Thread name "%s" is not valid.') ...
Waiting for all threads to appear, then continue. def exit_sync(self): ''' Waiting for all threads to appear, then continue. ''' if self._scan_threads and self.current_module_handle not in [t.name for t in self._scan_threads]: raise RuntimeError('Thread name "%s" is not valid.') ...
Running the FIFO readout while executing other statements. Starting and stopping of the FIFO readout is synchronized between the threads. def readout(self, args, *kwargs): ''' Running the FIFO readout while executing other statements. Starting and stopping of the FIFO readout is synchronize...
Starting the FIFO readout. Starting of the FIFO readout is executed only once by a random thread. Starting of the FIFO readout is synchronized between all threads reading out the FIFO. def start_readout(self, args, *kwargs): ''' Starting the FIFO readout. Starting of the FIFO readou...
Stopping the FIFO readout. Stopping of the FIFO readout is executed only once by a random thread. Stopping of the FIFO readout is synchronized between all threads reading out the FIFO. def stop_readout(self, timeout=10.0): ''' Stopping the FIFO readout. Stopping of the FIFO readout is...
Interpolatet the TDC calibration for each pixel from 0 to max_tdc def get_charge(max_tdc, tdc_calibration_values, tdc_pixel_calibration): # Return the charge from calibration ''' Interpolatet the TDC calibration for each pixel from 0 to max_tdc''' charge_calibration = np.zeros(shape=(80, 336, max_tdc)) fo...
Open the hit or calibration file and return the calibration per pixel def get_charge_calibration(calibation_file, max_tdc): ''' Open the hit or calibration file and return the calibration per pixel''' with tb.open_file(calibation_file, mode="r") as in_file_calibration_h5: tdc_calibration = in_file_cali...
Add the `Plot pyBAR data`. entry to `Dataset` menu. def addEntry(self): """Add the `Plot pyBAR data`. entry to `Dataset` menu. """ export_icon = QtGui.QIcon() pixmap = QtGui.QPixmap(os.path.join(PLUGINSDIR, 'csv/icons/document-export.png')) ...
Update the `export` QAction when the Dataset menu is pulled down. This method is a slot. See class ctor for details. def updateDatasetMenu(self): """Update the `export` QAction when the Dataset menu is pulled down. This method is a slot. See class ctor for details. """ enabled...
Export a given dataset to a `CSV` file. This method is a slot connected to the `export` QAction. See the :meth:`addEntry` method for details. def plot(self): """Export a given dataset to a `CSV` file. This method is a slot connected to the `export` QAction. See the :meth:`addE...
Brief description of the plugin. def helpAbout(self): """Brief description of the plugin. """ # Text to be displayed about_text = translate('pyBarPlugin', """<qt> <p>Data plotting plug-in for pyBAR. </qt>""", ...
Sends the config via ZeroMQ to a specified socket. Is called at the beginning of a run and when the config changes. Conf can be any config dictionary. def send_meta_data(socket, conf, name): '''Sends the config via ZeroMQ to a specified socket. Is called at the beginning of a run and when the config changes. Conf ...
Sends the data of every read out (raw data and meta data) via ZeroMQ to a specified socket def send_data(socket, data, scan_parameters={}, name='ReadoutData'): '''Sends the data of every read out (raw data and meta data) via ZeroMQ to a specified socket ''' if not scan_parameters: scan_parameters =...
Mimics pytables.open_file() and stores the configuration and run configuration Returns: RawDataFile Object Examples: with open_raw_data_file(filename = self.scan_data_filename, title=self.scan_id, scan_parameters=[scan_parameter]) as raw_data_file: # do something here raw_data_file.app...
Writing raw data file from data queue If you need to write raw data once in a while this function may make it easy for you. def save_raw_data_from_data_queue(data_queue, filename, mode='a', title='', scan_parameters=None): # mode="r+" to append data, raw_data_file_h5 must exist, "w" to overwrite raw_data_file_h5...
Metascript that calls other scripts to tune the FE. Parameters ---------- cfg_name : string Name of the config to be created. This config holds the tuning results. target_threshold : int The target threshold value in PlsrDAC. target_charge : int ...
Takes point data (x,y) with errors(x,y) and fits a straight line. The deviation to this line is also plotted, showing the offset. Parameters ---------- x, y, x_err, y_err: iterable filename: string, PdfPages object or None PdfPages file object: plot is appended to the pdf stri...
Takes 2D point data (x,y) and creates a profile histogram similar to the TProfile in ROOT. It calculates the y mean for every bin at the bin center and gives the y mean error as error bars. Parameters ---------- x : array like data x positions y : array like data y positions...
Rounding up to the nearest multiple of any positive integer Parameters ---------- number : int, float Input number. multiple : int Round up to multiple of multiple. Will be converted to int. Must not be equal zero. Returns ------- ceil_mod_number : int Rou...
Calculate quantiles from histograms, cuts off hist below and above given quantile. This function will not cut off more than the given values. Parameters ---------- hist : array_like, iterable Input histogram with dimension at most 1. prob : float, list, tuple List of quantiles to...
Find the last nonzero index and mask the remaining entries. Parameters ---------- hist : array_like, iterable Input histogram with dimension at most 1. return_index : bool, optional If true, return the index. copy : bool, optional Whether to copy the input data (Tru...
Readout thread continuously reading FIFO. Readout thread, which uses read_raw_data_from_fifo() and appends data to self._fifo_data_deque (collection.deque). def readout(self, fifo, no_data_timeout=None): '''Readout thread continuously reading FIFO. Readout thread, which uses read_raw_dat...
Worker thread continuously filtering and converting data when data becomes available. def worker(self, fifo): '''Worker thread continuously filtering and converting data when data becomes available. ''' logging.debug('Starting worker thread for %s', fifo) self._fifo_conditions[fifo]...
Writer thread continuously calling callback function for writing data when data becomes available. def writer(self, index, no_data_timeout=None): '''Writer thread continuously calling callback function for writing data when data becomes available. ''' is_fe_data_header = logical_and(is_fe_wo...
Reads local data buffer and returns data and meta data list. Returns ------- data : list List of data and meta data dicts. def get_data_from_buffer(self, filter_func=None, converter_func=None): '''Reads local data buffer and returns data and meta data list. ...
Reads local data buffer and returns raw data array. Returns ------- data : np.array An array containing data words from the local data buffer. def get_raw_data_from_buffer(self, filter_func=None, converter_func=None): '''Reads local data buffer and returns raw data ar...
Reads FIFO data and returns raw data array. Returns ------- data : np.array An array containing FIFO data words. def read_raw_data_from_fifo(self, fifo, filter_func=None, converter_func=None): '''Reads FIFO data and returns raw data array. Returns ...
Attempts to retrieve an item from the queue Q. If Q is empty, None is returned. Blocks for 'timeout' seconds in case the queue is empty, so don't use this method for speedy retrieval of multiple items (use get_all_from_queue for that). def get_item_from_queue(Q, timeout=0.01): ...
Return a list of elements of seq[i] with the lowest func(seq[i]) scores. >>> argmin_list(['one', 'to', 'three', 'or'], len) ['to', 'or'] def argmin_list(seq, func): """ Return a list of elements of seq[i] with the lowest func(seq[i]) scores. >>> argmin_list(['one', 'to...
flatten iterable, but leaves out strings [[[1, 2, 3], [4, 5]], 6] -> [1, 2, 3, 4, 5, 6] def flatten_iterable(iterable): """flatten iterable, but leaves out strings [[[1, 2, 3], [4, 5]], 6] -> [1, 2, 3, 4, 5, 6] """ for item in iterable: if isinstance(item, collections.Iterable) ...
generate iterable from item, but leaves out strings def iterable(item): """generate iterable from item, but leaves out strings """ if isinstance(item, collections.Iterable) and not isinstance(item, basestring): return item else: return [item]
Returns a copy of seq, sorted by natural string sort. def natsorted(seq, cmp=natcmp): "Returns a copy of seq, sorted by natural string sort." import copy temp = copy.copy(seq) natsort(temp, cmp) return temp
returns time as ISO string, mapping to and from datetime in ugly way convert to string with str() def get_iso_time(): '''returns time as ISO string, mapping to and from datetime in ugly way convert to string with str() ''' t1 = time.time() t2 = datetime.datetime.fromtimestamp(t1) ...
returns time as double precision floats - Time64 in pytables - mapping to and from python datetime's def get_float_time(): '''returns time as double precision floats - Time64 in pytables - mapping to and from python datetime's ''' t1 = time.time() t2 = datetime.datetime.fromtimestamp(t1) ret...
Group dict of dicts by key. def groupby_dict(dictionary, key): ''' Group dict of dicts by key. ''' return dict((k, list(g)) for k, g in itertools.groupby(sorted(dictionary.keys(), key=lambda name: dictionary[name][key]), key=lambda name: dictionary[name][key]))
Zipping iterables without fillvalue. Note: https://stackoverflow.com/questions/38054593/zip-longest-without-fillvalue def zip_nofill(*iterables): '''Zipping iterables without fillvalue. Note: https://stackoverflow.com/questions/38054593/zip-longest-without-fillvalue ''' return (tuple([entr...
Finding file in directory upwards. def find_file_dir_up(filename, path=None, n=None): '''Finding file in directory upwards. ''' if path is None: path = os.getcwd() i = 0 while True: current_path = path for _ in range(i): current_path = os.path.split(curr...
Loading configuration from text files to register object Parameters ---------- register : pybar.fei4.register object configuration_file : string Full path (directory and filename) of the configuration file. If name is not given, reload configuration from file. def load_configuration_from...
Loading configuration from HDF5 file to register object Parameters ---------- register : pybar.fei4.register object configuration_file : string, file Filename of the HDF5 configuration file or file object. node : string Additional identifier (subgroup). Useful when more than...
Saving configuration to text files from register object Parameters ---------- register : pybar.fei4.register object configuration_file : string Filename of the configuration file. def save_configuration_to_text_file(register, configuration_file): '''Saving configuration to text file...
Saving configuration to HDF5 file from register object Parameters ---------- register : pybar.fei4.register object configuration_file : string, file Filename of the HDF5 configuration file or file object. name : string Additional identifier (subgroup). Useful when storing mo...
Loading configuration Parameters ---------- configuration_file : string Path to the configuration file (text or HDF5 file). def load_configuration(self, configuration_file): '''Loading configuration Parameters ---------- configuration_file...
Saving configuration Parameters ---------- configuration_file : string Filename of the configuration file. def save_configuration(self, configuration_file): '''Saving configuration Parameters ---------- configuration_file : string ...
get fe_command from command name and keyword arguments wrapper for build_commands() implements FEI4 specific behavior def get_commands(self, command_name, **kwargs): """get fe_command from command name and keyword arguments wrapper for build_commands() implements FEI4 s...
build command from command_name and keyword values Returns ------- command_bitvector : list List of bitarrays. Usage ----- Receives: command name as defined inside xml file, key-value-pairs as defined inside bit stream filed for each command def bu...
Calculating register numbers from register names. Usage: get_global_register_attributes("attribute_name", name = [regname_1, regname_2, ...], addresses = 2) Receives: attribute name to be returned, dictionaries (kwargs) of register attributes and values for making cuts Returns: list of attr...
Generate register objects (list) from register name list Usage: get_global_register_objects(name = ["Amp2Vbn", "GateHitOr", "DisableColumnCnfg"], address = [2, 3]) Receives: keyword lists of register names, addresses,... for making cuts Returns: list of register objects def get_global_regi...
Calculating register bitsets from register addresses. Usage: get_global_register_bitsets([regaddress_1, regaddress_2, ...]) Receives: list of register addresses Returns: list of register bitsets def get_global_register_bitsets(self, register_addresses): # TOTO: add sorting """Cal...
Generate register objects (list) from register name list Usage: get_pixel_register_objects(name = ["TDAC", "FDAC"]) Receives: keyword lists of register names, addresses,... Returns: list of register objects def get_pixel_register_objects(self, do_sort=None, reverse=False, **kwargs): ...
Calculating pixel register bitsets from pixel register addresses. Usage: get_pixel_register_bitset(object, bit_number, double_column_number) Receives: register object, bit number, double column number Returns: double column bitset def get_pixel_register_bitset(self, register_object, bit_no...
Creating a configuration restore point. Parameters ---------- name : str Name of the restore point. If not given, a md5 hash will be generated. def create_restore_point(self, name=None): '''Creating a configuration restore point. Parameters -------...
Restoring a configuration restore point. Parameters ---------- name : str Name of the restore point. If not given, a md5 hash will be generated. keep : bool Keeping restore point for later use. last : bool If name is not given, the la...
Deleting all/a configuration restore points/point. Parameters ---------- name : str Name of the restore point to be deleted. If not given, all restore points will be deleted. def clear_restore_points(self, name=None): '''Deleting all/a configuration restore points/poi...
Stores any configuration dictionary to HDF5 file. Parameters ---------- h5_file : string, file Filename of the HDF5 configuration file or file object. configuation_name : str Configuration name. Will be used for table name. configuration : dict Configuration diction...
Filter and convert raw data numpy array (numpy.ndarray). Parameters ---------- array : numpy.array Raw data array. filter_func : function Function that takes array and returns true or false for each item in array. converter_func : function Function that takes array ...
Convert raw data in data iterable. Parameters ---------- data_iterable : iterable Iterable where each element is a tuple with following content: (raw data, timestamp_start, timestamp_stop, status). filter_func : function Function that takes array and returns true or false for eac...
Convert data iterable to raw data numpy array. Parameters ---------- data_iterable : iterable Iterable where each element is a tuple with following content: (raw data, timestamp_start, timestamp_stop, status). Returns ------- data_array : numpy.array concatenated data...
Converts TDC words at a given channel to common TDC header (0x4). def convert_tdc_to_channel(channel): ''' Converts TDC words at a given channel to common TDC header (0x4). ''' def f(value): filter_func = logical_and(is_tdc_word, is_tdc_from_channel(channel)) select = filter_func(value...
Selecting FE data from given channel. Parameters ---------- channel : int Channel number (4 is default channel on Single Chip Card). Returns ------- Function. Usage: 1 Selecting FE data from channel 4 (combine with is_fe_word): filter_fe_data_from_channel_...
Logical and from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. Usage: filter_func=logical_and(is_data_record, is_data_from_channel(4)) # new filter function ...
Logical or from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. def logical_or(f1, f2): # function factory '''Logical or from functions. Parameters -----...
Logical not from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. def logical_not(f): # function factory '''Logical not from functions. Parameters -------...
Logical xor from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. def logical_xor(f1, f2): # function factory '''Logical xor from functions. Parameters --...
Returns 31bit trigger counter (mode=0), 31bit timestamp (mode=1), 15bit timestamp and 16bit trigger counter (mode=2) def get_trigger_data(value, mode=0): '''Returns 31bit trigger counter (mode=0), 31bit timestamp (mode=1), 15bit timestamp and 16bit trigger counter (mode=2) ''' if mode == 2: ret...
Convert raw data array to column, row, and ToT array. Parameters ---------- array : numpy.array Raw data array. Returns ------- Tuple of arrays. def get_col_row_tot_array_from_data_record_array(array): # TODO: max ToT '''Convert raw data array to column, row, and ToT ar...
Takes the pixel raw data and interprets them. This includes consistency checks and pixel/data matching. The data has to come from one double column only but can have more than one pixel bit (e.g. TDAC = 5 bit). Parameters ---------- data : numpy.ndarray The raw data words. dc : int ...
Set all settings to their standard values. def set_standard_settings(self): '''Set all settings to their standard values. ''' if self.is_open(self.out_file_h5): self.out_file_h5.close() self.out_file_h5 = None self._setup_clusterizer() self.chunk_size = 30000...
Set the numbers of BCIDs (usually 16) of one event. def trig_count(self, value): """Set the numbers of BCIDs (usually 16) of one event.""" self._trig_count = 16 if value == 0 else value self.interpreter.set_trig_count(self._trig_count)
Set maximum ToT value that is considered to be a hit def max_tot_value(self, value): """Set maximum ToT value that is considered to be a hit""" self._max_tot_value = value self.interpreter.set_max_tot(self._max_tot_value) self.histogram.set_max_tot(self._max_tot_value) self.clus...
Interprets the raw data word table of all given raw data files with the c++ library. Creates the h5 output file and PDF plots. Parameters ---------- analyzed_data_file : string The file name of the output analyzed data file. If None, the output analyzed data file ...
Analyzes a hit table with the c++ histogrammming/clusterizer. Parameters ---------- analyzed_data_file : string The filename of the analyzed data file. If None, the analyzed data file specified during initialization is taken. Filename extension (.h5) does not...
Tries to get the scan parameters needed for analysis from the raw data file def _deduce_settings_from_file(self, opened_raw_data_file): # TODO: parse better '''Tries to get the scan parameters needed for analysis from the raw data file ''' try: # take infos raw data files (not avalable in old...
Takes the PlsrDAC calibration and the stored C-high/C-low mask to calculate the charge from the PlsrDAC array on a pixel basis def _get_plsr_dac_charge(self, plsr_dac_array, no_offset=False): '''Takes the PlsrDAC calibration and the stored C-high/C-low mask to calculate the charge from the PlsrDAC array on a p...
If Schema access, parse fields and build respective lists def _parse_fields(self, result, field_name): """ If Schema access, parse fields and build respective lists """ field_list = [] for key, value in result.get('schema', {}).get(field_name, {}).items(): if key not in fiel...
Builds a list of valid fields def _build_fields(self): """ Builds a list of valid fields """ declared_fields = self.solr._send_request('get', ADMIN_URL) result = decoder.decode(declared_fields) self.field_list = self._parse_fields(result, 'fields') # Build regular expre...
Reformats the given document before insertion into Solr. This method reformats the document in the following ways: - removes extraneous fields that aren't defined in schema.xml - unwinds arrays in order to find and later flatten sub-documents - flattens the document so that there ...
Override DocManagerBase.apply_update to have flat documents. def apply_update(self, doc, update_spec): """Override DocManagerBase.apply_update to have flat documents.""" # Replace a whole document if not '$set' in update_spec and not '$unset' in update_spec: # update_spec contains t...
Apply updates given in update_spec to the document whose id matches that of doc. def update(self, document_id, update_spec, namespace, timestamp): """Apply updates given in update_spec to the document whose id matches that of doc. """ # Commit outstanding changes so that the do...
Update or insert a document into Solr This method should call whatever add/insert/update method exists for the backend engine and add the document in there. The input will always be one mongo document, represented as a Python dictionary. def upsert(self, doc, namespace, timestamp): """...
Update or insert multiple documents into Solr docs may be any iterable def bulk_upsert(self, docs, namespace, timestamp): """Update or insert multiple documents into Solr docs may be any iterable """ if self.auto_commit_interval is not None: add_kwargs = { ...
Removes documents from Solr The input is a python dictionary that represents a mongo document. def remove(self, document_id, namespace, timestamp): """Removes documents from Solr The input is a python dictionary that represents a mongo document. """ self.solr.delete(id=u(docum...
Helper method for iterating over Solr search results. def _stream_search(self, query): """Helper method for iterating over Solr search results.""" for doc in self.solr.search(query, rows=100000000): if self.unique_key != "_id": doc["_id"] = doc.pop(self.unique_key) ...
Called to query Solr for documents in a time range. def search(self, start_ts, end_ts): """Called to query Solr for documents in a time range.""" query = '_ts: [%s TO %s]' % (start_ts, end_ts) return self._stream_search(query)
Returns the last document stored in the Solr engine. def get_last_doc(self): """Returns the last document stored in the Solr engine. """ #search everything, sort by descending timestamp, return 1 row try: result = self.solr.search(':', sort='_ts desc', rows=1) exce...
Returns the result of the Password-Based Key Derivation Function 2 with a single iteration (i.e. count = 1). prf - a psuedorandom function See http://en.wikipedia.org/wiki/PBKDF2 def pbkdf2_single(password, salt, key_length, prf): '''Returns the result of the Password-Based Key Derivation Fu...
Salsa 20/8 stream cypher; Used by BlockMix. See http://en.wikipedia.org/wiki/Salsa20 def salsa20_8(B): '''Salsa 20/8 stream cypher; Used by BlockMix. See http://en.wikipedia.org/wiki/Salsa20''' # Create a working copy x = B[:] # Expanded form of this code. The expansion is significantly faster but ...
Blockmix; Used by SMix. def blockmix_salsa8(BY, Yi, r): '''Blockmix; Used by SMix.''' start = (2 * r - 1) * 16 X = BY[start:start + 16] # BlockMix - 1 for i in xrange(0, 2 * r): # BlockMix - 2 for xi in xrange(0, 16): ...
SMix; a specific case of ROMix. See scrypt.pdf in the links above. def smix(B, Bi, r, N, V, X): '''SMix; a specific case of ROMix. See scrypt.pdf in the links above.''' X[:32 * r] = B[Bi:Bi + 32 * r] # ROMix - 1 for i in xrange(0, N): # ROMix - 2 aod = ...
Returns the result of the scrypt password-based key derivation function. Constraints: r * p < (2 30) dkLen <= (((2 32) - 1) * 32 N must be a power of 2 greater than 1 (eg. 2, 4, 8, 16, 32...) N, r, p must be positive def hash(password, salt, N, r, p, dkLen): """Ret...
Return an internal attribute after ensuring the headers is loaded if necessary. def _load_get_attr(self, name): 'Return an internal attribute after ensuring the headers is loaded if necessary.' if self._mode in _allowed_read and self._N is None: self._read_header() return getattr(se...
Close the underlying file. Sets data attribute .closed to True. A closed file cannot be used for further I/O operations. close() may be called more than once without error. Some kinds of file objects (for example, opened by popen()) may return an exit status upon closing. def close(sel...
Returns whether a scrypt encrypted file is valid. def verify_file(fp, password): 'Returns whether a scrypt encrypted file is valid.' sf = ScryptFile(fp = fp, password = password) for line in sf: pass sf.close() return sf.valid
Next line from the decrypted file, as a string. Retain newline. A non-negative size argument limits the maximum number of bytes to return (an incomplete line may be returned then). Return an empty string at EOF. def readline(self, size = None): '''Next line from the decrypted file, as...
Read and parse the header and calculate derived keys. def _read_header(self): '''Read and parse the header and calculate derived keys.''' try: # Read the entire header header = self._fp.read(96) if len(header) != 96: raise InvalidScryptFileFormat("In...
Read at most size bytes, returned as a string. If the size argument is negative or omitted, read until EOF is reached. Notice that when in non-blocking mode, less data than what was requested may be returned, even if no size parameter was given. def read(self, size = None): '''Read at ...
Writes the header to the underlying file object. def _write_header(self): 'Writes the header to the underlying file object.' header = b'scrypt' + CHR0 + struct.pack('>BII', int(math.log(self.N, 2)), self.r, self.p) + self.salt # Add the header checksum to the header checksum = hashlib...

Handling of Exceptions. Parameters ---------- exc : list, tuple Information of the exception of the format (type, value, traceback). Uses the return value of sys.exc_info(). def handle_err(self, exc): '''Handling of Exceptions. Parameters ------...

Returns the configuration for a given module ID. The working directory is searched for a file matching the module_id with the given run number. If no run number is defined the last successfull run defines the run number. def get_configuration(self, module_id, run_number=None): ''' Retu...

Select module and give access to the module. def select_module(self, module_id): ''' Select module and give access to the module. ''' if not isinstance(module_id, basestring) and isinstance(module_id, Iterable) and set(module_id) - set(self._modules): raise ValueError('Module IDs in...

Deselect module and cleanup. def deselect_module(self): ''' Deselect module and cleanup. ''' self._enabled_fe_channels = [] # ignore any RX sync errors self._readout_fifos = [] self._filter = [] self._converter = [] self.dut['TX']['OUTPUT_ENABLE'] = 0 se...

Waiting for all threads to appear, then continue. def enter_sync(self): ''' Waiting for all threads to appear, then continue. ''' if self._scan_threads and self.current_module_handle not in [t.name for t in self._scan_threads]: raise RuntimeError('Thread name "%s" is not valid.') ...

Waiting for all threads to appear, then continue. def exit_sync(self): ''' Waiting for all threads to appear, then continue. ''' if self._scan_threads and self.current_module_handle not in [t.name for t in self._scan_threads]: raise RuntimeError('Thread name "%s" is not valid.') ...

Running the FIFO readout while executing other statements. Starting and stopping of the FIFO readout is synchronized between the threads. def readout(self, *args, **kwargs): ''' Running the FIFO readout while executing other statements. Starting and stopping of the FIFO readout is synchronize...

Starting the FIFO readout. Starting of the FIFO readout is executed only once by a random thread. Starting of the FIFO readout is synchronized between all threads reading out the FIFO. def start_readout(self, *args, **kwargs): ''' Starting the FIFO readout. Starting of the FIFO readou...

Stopping the FIFO readout. Stopping of the FIFO readout is executed only once by a random thread. Stopping of the FIFO readout is synchronized between all threads reading out the FIFO. def stop_readout(self, timeout=10.0): ''' Stopping the FIFO readout. Stopping of the FIFO readout is...

Interpolatet the TDC calibration for each pixel from 0 to max_tdc def get_charge(max_tdc, tdc_calibration_values, tdc_pixel_calibration): # Return the charge from calibration ''' Interpolatet the TDC calibration for each pixel from 0 to max_tdc''' charge_calibration = np.zeros(shape=(80, 336, max_tdc)) fo...

Open the hit or calibration file and return the calibration per pixel def get_charge_calibration(calibation_file, max_tdc): ''' Open the hit or calibration file and return the calibration per pixel''' with tb.open_file(calibation_file, mode="r") as in_file_calibration_h5: tdc_calibration = in_file_cali...

Add the `Plot pyBAR data`. entry to `Dataset` menu. def addEntry(self): """Add the `Plot pyBAR data`. entry to `Dataset` menu. """ export_icon = QtGui.QIcon() pixmap = QtGui.QPixmap(os.path.join(PLUGINSDIR, 'csv/icons/document-export.png')) ...

Update the `export` QAction when the Dataset menu is pulled down. This method is a slot. See class ctor for details. def updateDatasetMenu(self): """Update the `export` QAction when the Dataset menu is pulled down. This method is a slot. See class ctor for details. """ enabled...

Export a given dataset to a `CSV` file. This method is a slot connected to the `export` QAction. See the :meth:`addEntry` method for details. def plot(self): """Export a given dataset to a `CSV` file. This method is a slot connected to the `export` QAction. See the :meth:`addE...

Brief description of the plugin. def helpAbout(self): """Brief description of the plugin. """ # Text to be displayed about_text = translate('pyBarPlugin', """<qt> <p>Data plotting plug-in for pyBAR. </qt>""", ...

Sends the config via ZeroMQ to a specified socket. Is called at the beginning of a run and when the config changes. Conf can be any config dictionary. def send_meta_data(socket, conf, name): '''Sends the config via ZeroMQ to a specified socket. Is called at the beginning of a run and when the config changes. Conf ...

Sends the data of every read out (raw data and meta data) via ZeroMQ to a specified socket def send_data(socket, data, scan_parameters={}, name='ReadoutData'): '''Sends the data of every read out (raw data and meta data) via ZeroMQ to a specified socket ''' if not scan_parameters: scan_parameters =...

Mimics pytables.open_file() and stores the configuration and run configuration Returns: RawDataFile Object Examples: with open_raw_data_file(filename = self.scan_data_filename, title=self.scan_id, scan_parameters=[scan_parameter]) as raw_data_file: # do something here raw_data_file.app...

Writing raw data file from data queue If you need to write raw data once in a while this function may make it easy for you. def save_raw_data_from_data_queue(data_queue, filename, mode='a', title='', scan_parameters=None): # mode="r+" to append data, raw_data_file_h5 must exist, "w" to overwrite raw_data_file_h5...

Metascript that calls other scripts to tune the FE. Parameters ---------- cfg_name : string Name of the config to be created. This config holds the tuning results. target_threshold : int The target threshold value in PlsrDAC. target_charge : int ...

Takes point data (x,y) with errors(x,y) and fits a straight line. The deviation to this line is also plotted, showing the offset. Parameters ---------- x, y, x_err, y_err: iterable filename: string, PdfPages object or None PdfPages file object: plot is appended to the pdf stri...

Takes 2D point data (x,y) and creates a profile histogram similar to the TProfile in ROOT. It calculates the y mean for every bin at the bin center and gives the y mean error as error bars. Parameters ---------- x : array like data x positions y : array like data y positions...

Rounding up to the nearest multiple of any positive integer Parameters ---------- number : int, float Input number. multiple : int Round up to multiple of multiple. Will be converted to int. Must not be equal zero. Returns ------- ceil_mod_number : int Rou...

Calculate quantiles from histograms, cuts off hist below and above given quantile. This function will not cut off more than the given values. Parameters ---------- hist : array_like, iterable Input histogram with dimension at most 1. prob : float, list, tuple List of quantiles to...

Find the last nonzero index and mask the remaining entries. Parameters ---------- hist : array_like, iterable Input histogram with dimension at most 1. return_index : bool, optional If true, return the index. copy : bool, optional Whether to copy the input data (Tru...

Readout thread continuously reading FIFO. Readout thread, which uses read_raw_data_from_fifo() and appends data to self._fifo_data_deque (collection.deque). def readout(self, fifo, no_data_timeout=None): '''Readout thread continuously reading FIFO. Readout thread, which uses read_raw_dat...

Worker thread continuously filtering and converting data when data becomes available. def worker(self, fifo): '''Worker thread continuously filtering and converting data when data becomes available. ''' logging.debug('Starting worker thread for %s', fifo) self._fifo_conditions[fifo]...

Writer thread continuously calling callback function for writing data when data becomes available. def writer(self, index, no_data_timeout=None): '''Writer thread continuously calling callback function for writing data when data becomes available. ''' is_fe_data_header = logical_and(is_fe_wo...

Reads local data buffer and returns data and meta data list. Returns ------- data : list List of data and meta data dicts. def get_data_from_buffer(self, filter_func=None, converter_func=None): '''Reads local data buffer and returns data and meta data list. ...

Reads local data buffer and returns raw data array. Returns ------- data : np.array An array containing data words from the local data buffer. def get_raw_data_from_buffer(self, filter_func=None, converter_func=None): '''Reads local data buffer and returns raw data ar...

Reads FIFO data and returns raw data array. Returns ------- data : np.array An array containing FIFO data words. def read_raw_data_from_fifo(self, fifo, filter_func=None, converter_func=None): '''Reads FIFO data and returns raw data array. Returns ...

Attempts to retrieve an item from the queue Q. If Q is empty, None is returned. Blocks for 'timeout' seconds in case the queue is empty, so don't use this method for speedy retrieval of multiple items (use get_all_from_queue for that). def get_item_from_queue(Q, timeout=0.01): ...

Return a list of elements of seq[i] with the lowest func(seq[i]) scores. >>> argmin_list(['one', 'to', 'three', 'or'], len) ['to', 'or'] def argmin_list(seq, func): """ Return a list of elements of seq[i] with the lowest func(seq[i]) scores. >>> argmin_list(['one', 'to...

flatten iterable, but leaves out strings [[[1, 2, 3], [4, 5]], 6] -> [1, 2, 3, 4, 5, 6] def flatten_iterable(iterable): """flatten iterable, but leaves out strings [[[1, 2, 3], [4, 5]], 6] -> [1, 2, 3, 4, 5, 6] """ for item in iterable: if isinstance(item, collections.Iterable) ...

generate iterable from item, but leaves out strings def iterable(item): """generate iterable from item, but leaves out strings """ if isinstance(item, collections.Iterable) and not isinstance(item, basestring): return item else: return [item]

Returns a copy of seq, sorted by natural string sort. def natsorted(seq, cmp=natcmp): "Returns a copy of seq, sorted by natural string sort." import copy temp = copy.copy(seq) natsort(temp, cmp) return temp

returns time as ISO string, mapping to and from datetime in ugly way convert to string with str() def get_iso_time(): '''returns time as ISO string, mapping to and from datetime in ugly way convert to string with str() ''' t1 = time.time() t2 = datetime.datetime.fromtimestamp(t1) ...

returns time as double precision floats - Time64 in pytables - mapping to and from python datetime's def get_float_time(): '''returns time as double precision floats - Time64 in pytables - mapping to and from python datetime's ''' t1 = time.time() t2 = datetime.datetime.fromtimestamp(t1) ret...

Group dict of dicts by key. def groupby_dict(dictionary, key): ''' Group dict of dicts by key. ''' return dict((k, list(g)) for k, g in itertools.groupby(sorted(dictionary.keys(), key=lambda name: dictionary[name][key]), key=lambda name: dictionary[name][key]))

Zipping iterables without fillvalue. Note: https://stackoverflow.com/questions/38054593/zip-longest-without-fillvalue def zip_nofill(*iterables): '''Zipping iterables without fillvalue. Note: https://stackoverflow.com/questions/38054593/zip-longest-without-fillvalue ''' return (tuple([entr...

Finding file in directory upwards. def find_file_dir_up(filename, path=None, n=None): '''Finding file in directory upwards. ''' if path is None: path = os.getcwd() i = 0 while True: current_path = path for _ in range(i): current_path = os.path.split(curr...

Loading configuration from text files to register object Parameters ---------- register : pybar.fei4.register object configuration_file : string Full path (directory and filename) of the configuration file. If name is not given, reload configuration from file. def load_configuration_from...

Loading configuration from HDF5 file to register object Parameters ---------- register : pybar.fei4.register object configuration_file : string, file Filename of the HDF5 configuration file or file object. node : string Additional identifier (subgroup). Useful when more than...

Saving configuration to text files from register object Parameters ---------- register : pybar.fei4.register object configuration_file : string Filename of the configuration file. def save_configuration_to_text_file(register, configuration_file): '''Saving configuration to text file...

Saving configuration to HDF5 file from register object Parameters ---------- register : pybar.fei4.register object configuration_file : string, file Filename of the HDF5 configuration file or file object. name : string Additional identifier (subgroup). Useful when storing mo...

Loading configuration Parameters ---------- configuration_file : string Path to the configuration file (text or HDF5 file). def load_configuration(self, configuration_file): '''Loading configuration Parameters ---------- configuration_file...

Saving configuration Parameters ---------- configuration_file : string Filename of the configuration file. def save_configuration(self, configuration_file): '''Saving configuration Parameters ---------- configuration_file : string ...

get fe_command from command name and keyword arguments wrapper for build_commands() implements FEI4 specific behavior def get_commands(self, command_name, **kwargs): """get fe_command from command name and keyword arguments wrapper for build_commands() implements FEI4 s...

build command from command_name and keyword values Returns ------- command_bitvector : list List of bitarrays. Usage ----- Receives: command name as defined inside xml file, key-value-pairs as defined inside bit stream filed for each command def bu...

Calculating register numbers from register names. Usage: get_global_register_attributes("attribute_name", name = [regname_1, regname_2, ...], addresses = 2) Receives: attribute name to be returned, dictionaries (kwargs) of register attributes and values for making cuts Returns: list of attr...

Generate register objects (list) from register name list Usage: get_global_register_objects(name = ["Amp2Vbn", "GateHitOr", "DisableColumnCnfg"], address = [2, 3]) Receives: keyword lists of register names, addresses,... for making cuts Returns: list of register objects def get_global_regi...

Calculating register bitsets from register addresses. Usage: get_global_register_bitsets([regaddress_1, regaddress_2, ...]) Receives: list of register addresses Returns: list of register bitsets def get_global_register_bitsets(self, register_addresses): # TOTO: add sorting """Cal...

Generate register objects (list) from register name list Usage: get_pixel_register_objects(name = ["TDAC", "FDAC"]) Receives: keyword lists of register names, addresses,... Returns: list of register objects def get_pixel_register_objects(self, do_sort=None, reverse=False, **kwargs): ...

Calculating pixel register bitsets from pixel register addresses. Usage: get_pixel_register_bitset(object, bit_number, double_column_number) Receives: register object, bit number, double column number Returns: double column bitset def get_pixel_register_bitset(self, register_object, bit_no...

Creating a configuration restore point. Parameters ---------- name : str Name of the restore point. If not given, a md5 hash will be generated. def create_restore_point(self, name=None): '''Creating a configuration restore point. Parameters -------...

Restoring a configuration restore point. Parameters ---------- name : str Name of the restore point. If not given, a md5 hash will be generated. keep : bool Keeping restore point for later use. last : bool If name is not given, the la...

Deleting all/a configuration restore points/point. Parameters ---------- name : str Name of the restore point to be deleted. If not given, all restore points will be deleted. def clear_restore_points(self, name=None): '''Deleting all/a configuration restore points/poi...

Stores any configuration dictionary to HDF5 file. Parameters ---------- h5_file : string, file Filename of the HDF5 configuration file or file object. configuation_name : str Configuration name. Will be used for table name. configuration : dict Configuration diction...

Filter and convert raw data numpy array (numpy.ndarray). Parameters ---------- array : numpy.array Raw data array. filter_func : function Function that takes array and returns true or false for each item in array. converter_func : function Function that takes array ...

Convert raw data in data iterable. Parameters ---------- data_iterable : iterable Iterable where each element is a tuple with following content: (raw data, timestamp_start, timestamp_stop, status). filter_func : function Function that takes array and returns true or false for eac...

Convert data iterable to raw data numpy array. Parameters ---------- data_iterable : iterable Iterable where each element is a tuple with following content: (raw data, timestamp_start, timestamp_stop, status). Returns ------- data_array : numpy.array concatenated data...

Converts TDC words at a given channel to common TDC header (0x4). def convert_tdc_to_channel(channel): ''' Converts TDC words at a given channel to common TDC header (0x4). ''' def f(value): filter_func = logical_and(is_tdc_word, is_tdc_from_channel(channel)) select = filter_func(value...

Selecting FE data from given channel. Parameters ---------- channel : int Channel number (4 is default channel on Single Chip Card). Returns ------- Function. Usage: 1 Selecting FE data from channel 4 (combine with is_fe_word): filter_fe_data_from_channel_...

Logical and from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. Usage: filter_func=logical_and(is_data_record, is_data_from_channel(4)) # new filter function ...

Logical or from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. def logical_or(f1, f2): # function factory '''Logical or from functions. Parameters -----...

Logical not from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. def logical_not(f): # function factory '''Logical not from functions. Parameters -------...

Logical xor from functions. Parameters ---------- f1, f2 : function Function that takes array and returns true or false for each item in array. Returns ------- Function. def logical_xor(f1, f2): # function factory '''Logical xor from functions. Parameters --...

Returns 31bit trigger counter (mode=0), 31bit timestamp (mode=1), 15bit timestamp and 16bit trigger counter (mode=2) def get_trigger_data(value, mode=0): '''Returns 31bit trigger counter (mode=0), 31bit timestamp (mode=1), 15bit timestamp and 16bit trigger counter (mode=2) ''' if mode == 2: ret...

Convert raw data array to column, row, and ToT array. Parameters ---------- array : numpy.array Raw data array. Returns ------- Tuple of arrays. def get_col_row_tot_array_from_data_record_array(array): # TODO: max ToT '''Convert raw data array to column, row, and ToT ar...

Takes the pixel raw data and interprets them. This includes consistency checks and pixel/data matching. The data has to come from one double column only but can have more than one pixel bit (e.g. TDAC = 5 bit). Parameters ---------- data : numpy.ndarray The raw data words. dc : int ...

Set all settings to their standard values. def set_standard_settings(self): '''Set all settings to their standard values. ''' if self.is_open(self.out_file_h5): self.out_file_h5.close() self.out_file_h5 = None self._setup_clusterizer() self.chunk_size = 30000...

Set the numbers of BCIDs (usually 16) of one event. def trig_count(self, value): """Set the numbers of BCIDs (usually 16) of one event.""" self._trig_count = 16 if value == 0 else value self.interpreter.set_trig_count(self._trig_count)

Set maximum ToT value that is considered to be a hit def max_tot_value(self, value): """Set maximum ToT value that is considered to be a hit""" self._max_tot_value = value self.interpreter.set_max_tot(self._max_tot_value) self.histogram.set_max_tot(self._max_tot_value) self.clus...

Interprets the raw data word table of all given raw data files with the c++ library. Creates the h5 output file and PDF plots. Parameters ---------- analyzed_data_file : string The file name of the output analyzed data file. If None, the output analyzed data file ...

Analyzes a hit table with the c++ histogrammming/clusterizer. Parameters ---------- analyzed_data_file : string The filename of the analyzed data file. If None, the analyzed data file specified during initialization is taken. Filename extension (.h5) does not...

Tries to get the scan parameters needed for analysis from the raw data file def _deduce_settings_from_file(self, opened_raw_data_file): # TODO: parse better '''Tries to get the scan parameters needed for analysis from the raw data file ''' try: # take infos raw data files (not avalable in old...

Takes the PlsrDAC calibration and the stored C-high/C-low mask to calculate the charge from the PlsrDAC array on a pixel basis def _get_plsr_dac_charge(self, plsr_dac_array, no_offset=False): '''Takes the PlsrDAC calibration and the stored C-high/C-low mask to calculate the charge from the PlsrDAC array on a p...

If Schema access, parse fields and build respective lists def _parse_fields(self, result, field_name): """ If Schema access, parse fields and build respective lists """ field_list = [] for key, value in result.get('schema', {}).get(field_name, {}).items(): if key not in fiel...

Builds a list of valid fields def _build_fields(self): """ Builds a list of valid fields """ declared_fields = self.solr._send_request('get', ADMIN_URL) result = decoder.decode(declared_fields) self.field_list = self._parse_fields(result, 'fields') # Build regular expre...

Reformats the given document before insertion into Solr. This method reformats the document in the following ways: - removes extraneous fields that aren't defined in schema.xml - unwinds arrays in order to find and later flatten sub-documents - flattens the document so that there ...

Override DocManagerBase.apply_update to have flat documents. def apply_update(self, doc, update_spec): """Override DocManagerBase.apply_update to have flat documents.""" # Replace a whole document if not '$set' in update_spec and not '$unset' in update_spec: # update_spec contains t...

Apply updates given in update_spec to the document whose id matches that of doc. def update(self, document_id, update_spec, namespace, timestamp): """Apply updates given in update_spec to the document whose id matches that of doc. """ # Commit outstanding changes so that the do...

Update or insert a document into Solr This method should call whatever add/insert/update method exists for the backend engine and add the document in there. The input will always be one mongo document, represented as a Python dictionary. def upsert(self, doc, namespace, timestamp): """...

Update or insert multiple documents into Solr docs may be any iterable def bulk_upsert(self, docs, namespace, timestamp): """Update or insert multiple documents into Solr docs may be any iterable """ if self.auto_commit_interval is not None: add_kwargs = { ...

Removes documents from Solr The input is a python dictionary that represents a mongo document. def remove(self, document_id, namespace, timestamp): """Removes documents from Solr The input is a python dictionary that represents a mongo document. """ self.solr.delete(id=u(docum...

Helper method for iterating over Solr search results. def _stream_search(self, query): """Helper method for iterating over Solr search results.""" for doc in self.solr.search(query, rows=100000000): if self.unique_key != "_id": doc["_id"] = doc.pop(self.unique_key) ...

Called to query Solr for documents in a time range. def search(self, start_ts, end_ts): """Called to query Solr for documents in a time range.""" query = '_ts: [%s TO %s]' % (start_ts, end_ts) return self._stream_search(query)

Returns the last document stored in the Solr engine. def get_last_doc(self): """Returns the last document stored in the Solr engine. """ #search everything, sort by descending timestamp, return 1 row try: result = self.solr.search('*:*', sort='_ts desc', rows=1) exce...

Returns the result of the Password-Based Key Derivation Function 2 with a single iteration (i.e. count = 1). prf - a psuedorandom function See http://en.wikipedia.org/wiki/PBKDF2 def pbkdf2_single(password, salt, key_length, prf): '''Returns the result of the Password-Based Key Derivation Fu...

Salsa 20/8 stream cypher; Used by BlockMix. See http://en.wikipedia.org/wiki/Salsa20 def salsa20_8(B): '''Salsa 20/8 stream cypher; Used by BlockMix. See http://en.wikipedia.org/wiki/Salsa20''' # Create a working copy x = B[:] # Expanded form of this code. The expansion is significantly faster but ...

Blockmix; Used by SMix. def blockmix_salsa8(BY, Yi, r): '''Blockmix; Used by SMix.''' start = (2 * r - 1) * 16 X = BY[start:start + 16] # BlockMix - 1 for i in xrange(0, 2 * r): # BlockMix - 2 for xi in xrange(0, 16): ...

SMix; a specific case of ROMix. See scrypt.pdf in the links above. def smix(B, Bi, r, N, V, X): '''SMix; a specific case of ROMix. See scrypt.pdf in the links above.''' X[:32 * r] = B[Bi:Bi + 32 * r] # ROMix - 1 for i in xrange(0, N): # ROMix - 2 aod = ...

Returns the result of the scrypt password-based key derivation function. Constraints: r * p < (2 ** 30) dkLen <= (((2 ** 32) - 1) * 32 N must be a power of 2 greater than 1 (eg. 2, 4, 8, 16, 32...) N, r, p must be positive def hash(password, salt, N, r, p, dkLen): """Ret...

Return an internal attribute after ensuring the headers is loaded if necessary. def _load_get_attr(self, name): 'Return an internal attribute after ensuring the headers is loaded if necessary.' if self._mode in _allowed_read and self._N is None: self._read_header() return getattr(se...

Close the underlying file. Sets data attribute .closed to True. A closed file cannot be used for further I/O operations. close() may be called more than once without error. Some kinds of file objects (for example, opened by popen()) may return an exit status upon closing. def close(sel...

Returns whether a scrypt encrypted file is valid. def verify_file(fp, password): 'Returns whether a scrypt encrypted file is valid.' sf = ScryptFile(fp = fp, password = password) for line in sf: pass sf.close() return sf.valid

Next line from the decrypted file, as a string. Retain newline. A non-negative size argument limits the maximum number of bytes to return (an incomplete line may be returned then). Return an empty string at EOF. def readline(self, size = None): '''Next line from the decrypted file, as...

Read and parse the header and calculate derived keys. def _read_header(self): '''Read and parse the header and calculate derived keys.''' try: # Read the entire header header = self._fp.read(96) if len(header) != 96: raise InvalidScryptFileFormat("In...

Read at most size bytes, returned as a string. If the size argument is negative or omitted, read until EOF is reached. Notice that when in non-blocking mode, less data than what was requested may be returned, even if no size parameter was given. def read(self, size = None): '''Read at ...

Writes the header to the underlying file object. def _write_header(self): 'Writes the header to the underlying file object.' header = b'scrypt' + CHR0 + struct.pack('>BII', int(math.log(self.N, 2)), self.r, self.p) + self.salt # Add the header checksum to the header checksum = hashlib...