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def _setup_launch(self): """ Method to be used by all launchers that prepares the root directory and generate basic launch information for command templates to use (including a registered timestamp). """ self.root_directory = self.get_root_directory() if not os.pa...
def _launch_process_group(self, process_commands, streams_path): """ Launches processes defined by process_commands, but only executes max_concurrency processes at a time; if a process completes and there are still outstanding processes to be executed, the next processes are run ...
def summary(self): """ A succinct summary of the Launcher configuration. Unlike the repr, a summary does not have to be complete but must supply key information relevant to the user. """ print("Type: %s" % self.__class__.__name__) print("Batch Name: %r" % self.ba...
def _qsub_args(self, override_options, cmd_args, append_options=[]): """ Method to generate Popen style argument list for qsub using the qsub_switches and qsub_flag_options parameters. Switches are returned first. The qsub_flag_options follow in keys() ordered if not a vanilla Py...
def collate_and_launch(self): """ Method that collates the previous jobs and launches the next block of concurrent jobs when using DynamicArgs. This method is invoked on initial launch and then subsequently via a commandline call (to Python via qsub) to collate the previo...
def _qsub_collate_and_launch(self, output_dir, error_dir, job_names): """ The method that actually runs qsub to invoke the python process with the necessary commands to trigger the next collation step and next block of jobs. """ job_name = "%s_%s_collate_%d" % (self.batc...
def _qsub_block(self, output_dir, error_dir, tid_specs): """ This method handles static argument specifiers and cases where the dynamic specifiers cannot be queued before the arguments are known. """ processes = [] job_names = [] for (tid, spec) in tid_sp...
def qdel_batch(self): """ Runs qdel command to remove all remaining queued jobs using the <batch_name>* pattern . Necessary when StopIteration is raised with scheduled jobs left on the queue. Returns exit-code of qdel. """ p = subprocess.Popen(['qdel', '%s_%s*' % ...
def _launch_process_group(self, process_commands, streams_path): """ Aggregates all process_commands and the designated output files into a list, and outputs it as JSON, after which the wrapper script is called. """ processes = [] for cmd, tid in process_commands: ...
def cross_check_launchers(self, launchers): """ Performs consistency checks across all the launchers. """ if len(launchers) == 0: raise Exception('Empty launcher list') timestamps = [launcher.timestamp for launcher in launchers] if not all(timestamps[0] == tstamp for tst...
def _launch_all(self, launchers): """ Launches all available launchers. """ for launcher in launchers: print("== Launching %s ==" % launcher.batch_name) launcher() return True
def _review_all(self, launchers): """ Runs the review process for all the launchers. """ # Run review of launch args if necessary if self.launch_args is not None: proceed = self.review_args(self.launch_args, show_repr=True, ...
def review_args(self, obj, show_repr=False, heading='Arguments'): """ Reviews the given argument specification. Can review the meta-arguments (launch_args) or the arguments themselves. """ args = obj.args if isinstance(obj, Launcher) else obj print('\n%s\n' % self.summary...
def input_options(self, options, prompt='Select option', default=None): """ Helper to prompt the user for input on the commandline. """ check_options = [x.lower() for x in options] while True: response = input('%s [%s]: ' % (prompt, ', '.join(options))).lower() ...
def save(self, filename, metadata={}, **data): """ The implementation in the base class simply checks there is no clash between the metadata and data keys. """ intersection = set(metadata.keys()) & set(data.keys()) if intersection: msg = 'Key(s) overlap betwe...
def _savepath(self, filename): """ Returns the full path for saving the file, adding an extension and making the filename unique as necessary. """ (basename, ext) = os.path.splitext(filename) basename = basename if (ext in self.extensions) else filename ext = ext ...
def file_supported(cls, filename): """ Returns a boolean indicating whether the filename has an appropriate extension for this class. """ if not isinstance(filename, str): return False (_, ext) = os.path.splitext(filename) if ext not in cls.extensions:...
def save(self, filename, imdata, **data): """ Data may be either a PIL Image object or a Numpy array. """ if isinstance(imdata, numpy.ndarray): imdata = Image.fromarray(numpy.uint8(imdata)) elif isinstance(imdata, Image.Image): imdata.save(self._savepath(f...
def fileModifiedTimestamp(fname): """return "YYYY-MM-DD" when the file was modified.""" modifiedTime=os.path.getmtime(fname) stamp=time.strftime('%Y-%m-%d', time.localtime(modifiedTime)) return stamp
def loadResults(resultsFile): """returns a dict of active folders with days as keys.""" with open(resultsFile) as f: raw=f.read().split("\n") foldersByDay={} for line in raw: folder=line.split('"')[1]+"\\" line=[]+line.split('"')[2].split(", ") for day in line[1:]...
def HTML_results(resultsFile): """generates HTML report of active folders/days.""" foldersByDay=loadResults(resultsFile) # optionally skip dates before a certain date # for day in sorted(list(foldersByDay.keys())): # if time.strptime(day,"%Y-%m-%d")<time.strptime("2016-05-01","%Y-%m-%d"): ...
def quietParts(data,percentile=10): """ Given some data (Y) break it into chunks and return just the quiet ones. Returns data where the variance for its chunk size is below the given percentile. CHUNK_POINTS should be adjusted so it's about 10ms of data. """ nChunks=int(len(Y)/CHUNK_POINTS) ...
def ndist(data,Xs): """ given some data and a list of X posistions, return the normal distribution curve as a Y point at each of those Xs. """ sigma=np.sqrt(np.var(data)) center=np.average(data) curve=mlab.normpdf(Xs,center,sigma) curve*=len(data)*HIST_RESOLUTION return curve
def abfinfo(self,printToo=False,returnDict=False): """show basic info about ABF class variables.""" info="\n### ABF INFO ###\n" d={} for thingName in sorted(dir(self)): if thingName in ['cm','evIs','colormap','dataX','dataY', 'protoX','protoY']: ...
def headerHTML(self,fname=None): """read the ABF header and save it HTML formatted.""" if fname is None: fname = self.fname.replace(".abf","_header.html") html="<html><body><code>" html+="<h2>abfinfo() for %s.abf</h2>"%self.ID html+=self.abfinfo().replace("<","&lt;")....
def generate_colormap(self,colormap=None,reverse=False): """use 1 colormap for the whole abf. You can change it!.""" if colormap is None: colormap = pylab.cm.Dark2 self.cm=colormap self.colormap=[] for i in range(self.sweeps): #TODO: make this the only colormap ...
def setSweep(self,sweep=0,force=False): """Load X/Y data for a particular sweep. determines if forced reload is needed, updates currentSweep, regenerates dataX (if not None),decimates,returns X/Y. Note that setSweep() takes 0.17ms to complete, so go for it! """ if sweep i...
def sweep_genXs(self): """generate sweepX (in seconds) to match sweepY""" if self.decimateMethod: self.dataX=np.arange(len(self.dataY))/self.rate self.dataX*=self.decimateBy return if self.dataX is None or len(self.dataX)!=len(self.dataY): self.dat...
def sweep_decimate(self): """ decimate data using one of the following methods: 'avg','max','min','fast' They're self explainatory. 'fast' just plucks the n'th data point. """ if len(self.dataY)<self.decimateBy: return if self.decimateMethod: ...
def get_data_around(self,timePoints,thisSweep=False,padding=0.02,msDeriv=0): """ return self.dataY around a time point. All units are seconds. if thisSweep==False, the time point is considered to be experiment time and an appropriate sweep may be selected. i.e., with 10 second ...
def generate_protocol(self,sweep=None): """ Create (x,y) points necessary to graph protocol for the current sweep. """ #TODO: make a line protocol that's plottable if sweep is None: sweep = self.currentSweep if sweep is None: sweep = 0 if n...
def clampValues(self,timePoint=0): """ return an array of command values at a time point (in sec). Useful for things like generating I/V curves. """ Cs=np.zeros(self.sweeps) for i in range(self.sweeps): self.setSweep(i) #TODO: protocol only = True ...
def guess_protocol(self): """ This just generates a string to define the nature of the ABF. The ultimate goal is to use info about the abf to guess what to do with it. [vc/ic]-[steps/fixed]-[notag/drugs]-[2ch/1ch] This represents 2^4 (18) combinations, but is easily expan...
def average_sweep(self,T1=0,T2=None,sweeps=None,stdErr=False): """ given an array of sweeps, return X,Y,Err average. This returns *SWEEPS* of data, not just 1 data point. """ T1=T1*self.rate if T2 is None: T2 = self.sweepSize-1 else: T2 = T...
def average_data(self,ranges=[[None,None]],percentile=None): """ given a list of ranges, return single point averages for every sweep. Units are in seconds. Expects something like: ranges=[[1,2],[4,5],[7,7.5]] None values will be replaced with maximum/minimum bounds. ...
def filter_gaussian(self,sigmaMs=100,applyFiltered=False,applyBaseline=False): """RETURNS filtered trace. Desn't filter it in place.""" if sigmaMs==0: return self.dataY filtered=cm.filter_gaussian(self.dataY,sigmaMs) if applyBaseline: self.dataY=self.dataY-filtere...
def saveThing(self,thing,fname,overwrite=True,ext=".pkl"): """save any object as /swhlab4/ID_[fname].pkl""" if not os.path.exists(os.path.dirname(self.outpre)): os.mkdir(os.path.dirname(self.outpre)) if ext and not ext in fname: fname+=ext fname=self.outpre+fname ...
def loadThing(self,fname,ext=".pkl"): """save any object from /swhlab4/ID_[fname].pkl""" if ext and not ext in fname: fname+=ext fname=self.outpre+fname time1=cm.timethis() thing = pickle.load(open(fname,"rb")) print(" -> loading [%s] (%.01f kB) took %.02f ms"...
def deleteStuff(self,ext="*",spareInfo=True,spare=["_info.pkl"]): """delete /swhlab4/ID_*""" print(" -- deleting /swhlab4/"+ext) for fname in sorted(glob.glob(self.outpre+ext)): reallyDelete=True for item in spare: if item in fname: rea...
def validate_activatable_models(): """ Raises a ValidationError for any ActivatableModel that has ForeignKeys or OneToOneFields that will cause cascading deletions to occur. This function also raises a ValidationError if the activatable model has not defined a Boolean field with the field name defined b...
def to_table(args, vdims=[]): "Helper function to convet an Args object to a HoloViews Table" if not Table: return "HoloViews Table not available" kdims = [dim for dim in args.constant_keys + args.varying_keys if dim not in vdims] items = [tuple([spec[k] for k in kdims+vdims]) ...
def pprint_args(self, pos_args, keyword_args, infix_operator=None, extra_params={}): """ Method to define the positional arguments and keyword order for pretty printing. """ if infix_operator and not (len(pos_args)==2 and keyword_args==[]): raise Exception('Infix form...
def _pprint(self, cycle=False, flat=False, annotate=False, onlychanged=True, level=1, tab = ' '): """ Pretty printer that prints only the modified keywords and generates flat representations (for repr) and optionally annotates the top of the repr with a comment. """ (kw...
def spec_formatter(cls, spec): " Formats the elements of an argument set appropriately" return type(spec)((k, str(v)) for (k,v) in spec.items())
def _collect_by_key(self,specs): """ Returns a dictionary like object with the lists of values collapsed by their respective key. Useful to find varying vs constant keys and to find how fast keys vary. """ # Collect (key, value) tuples as list of lists, flatten with chain...
def _cartesian_product(self, first_specs, second_specs): """ Takes the Cartesian product of the specifications. Result will contain N specifications where N = len(first_specs) * len(second_specs) and keys are merged. Example: [{'a':1},{'b':2}] * [{'c':3},{'d':4}] = [{'a':...
def summary(self): """ A succinct summary of the argument specifier. Unlike the repr, a summary does not have to be complete but must supply the most relevant information about the object to the user. """ print("Items: %s" % len(self)) varying_keys = ', '.join('%r...
def _build_specs(self, specs, kwargs, fp_precision): """ Returns the specs, the remaining kwargs and whether or not the constructor was called with kwarg or explicit specs. """ if specs is None: overrides = param.ParamOverrides(self, kwargs, ...
def _unique(self, sequence, idfun=repr): """ Note: repr() must be implemented properly on all objects. This is implicitly assumed by Lancet when Python objects need to be formatted to string representation. """ seen = {} return [seen.setdefault(idfun(e),e) for e i...
def show(self, exclude=[]): """ Convenience method to inspect the available argument values in human-readable format. The ordering of keys is determined by how quickly they vary. The exclude list allows specific keys to be excluded for readability (e.g. to hide long, abs...
def lexsort(self, *order): """ The lexical sort order is specified by a list of string arguments. Each string is a key name prefixed by '+' or '-' for ascending and descending sort respectively. If the key is not found in the operand's set of varying keys, it is ignored. ...
def _lexsorted_specs(self, order): """ A lexsort is specified using normal key string prefixed by '+' (for ascending) or '-' for (for descending). Note that in Python 2, if a key is missing, None is returned (smallest Python value). In Python 3, an Exception will be rais...
def linspace(self, start, stop, n): """ Simple replacement for numpy linspace""" if n == 1: return [start] L = [0.0] * n nm1 = n - 1 nm1inv = 1.0 / nm1 for i in range(n): L[i] = nm1inv * (start*(nm1 - i) + stop*i) return L
def extract_log(log_path, dict_type=dict): """ Parses the log file generated by a launcher and returns dictionary with tid keys and specification values. Ordering can be maintained by setting dict_type to the appropriate constructor (i.e. OrderedDict). Keys are converted ...
def write_log(log_path, data, allow_append=True): """ Writes the supplied specifications to the log path. The data may be supplied as either as a an Args or as a list of dictionaries. By default, specifications will be appropriately appended to an existing log file. This...
def directory(cls, directory, root=None, extension=None, **kwargs): """ Load all the files in a given directory selecting only files with the given extension if specified. The given kwargs are passed through to the normal constructor. """ root = os.getcwd() if root is Non...
def fields(self): """ Return the fields specified in the pattern using Python's formatting mini-language. """ parse = list(string.Formatter().parse(self.pattern)) return [f for f in zip(*parse)[1] if f is not None]
def _load_expansion(self, key, root, pattern): """ Loads the files that match the given pattern. """ path_pattern = os.path.join(root, pattern) expanded_paths = self._expand_pattern(path_pattern) specs=[] for (path, tags) in expanded_paths: filelist =...
def _expand_pattern(self, pattern): """ From the pattern decomposition, finds the absolute paths matching the pattern. """ (globpattern, regexp, fields, types) = self._decompose_pattern(pattern) filelist = glob.glob(globpattern) expansion = [] for fname i...
def _decompose_pattern(self, pattern): """ Given a path pattern with format declaration, generates a four-tuple (glob_pattern, regexp pattern, fields, type map) """ sep = '~lancet~sep~' float_codes = ['e','E','f', 'F','g', 'G', 'n'] typecodes = dict([(k,float) for...
def from_pattern(cls, pattern, filetype=None, key='filename', root=None, ignore=[]): """ Convenience method to directly chain a pattern processed by FilePattern into a FileInfo instance. Note that if a default filetype has been set on FileInfo, the filetype argument may be omitt...
def load(self, val, **kwargs): """ Load the file contents into the supplied pandas dataframe or HoloViews Table. This allows a selection to be made over the metadata before loading the file contents (may be slow). """ if Table and isinstance(val, Table): retur...
def load_table(self, table): """ Load the file contents into the supplied Table using the specified key and filetype. The input table should have the filenames as values which will be replaced by the loaded data. If data_key is specified, this key will be used to index th...
def load_dframe(self, dframe): """ Load the file contents into the supplied dataframe using the specified key and filetype. """ filename_series = dframe[self.key] loaded_data = filename_series.map(self.filetype.data) keys = [list(el.keys()) for el in loaded_data.v...
def _info(self, source, key, filetype, ignore): """ Generates the union of the source.specs and the metadata dictionary loaded by the filetype object. """ specs, mdata = [], {} mdata_clashes = set() for spec in source.specs: if key not in spec: ...
async def _push(self, *args, **kwargs): """Push new data into the buffer. Resume looping if paused.""" self._data.append((args, kwargs)) if self._future is not None: future, self._future = self._future, None future.set_result(True)
def newVersion(): """increments version counter in swhlab/version.py""" version=None fname='../swhlab/version.py' with open(fname) as f: raw=f.read().split("\n") for i,line in enumerate(raw): if line.startswith("__counter__"): if version is None: ...
def figureStimulus(abf,sweeps=[0]): """ Create a plot of one area of interest of a single sweep. """ stimuli=[2.31250, 2.35270] for sweep in sweeps: abf.setsweep(sweep) for stimulus in stimuli: S1=int(abf.pointsPerSec*stimulus) S2=int(abf.pointsPerSec*(stimul...
def phasicTonic(self,m1=None,m2=None,chunkMs=50, quietPercentile=10,histResolution=1): """ chunkMs should be ~50 ms or greater. bin sizes must be equal to or multiples of the data resolution. transients smaller than the expected RMS will be silenced. """ ...
def doStuff(ABFfolder,analyze=False,convert=False,index=True,overwrite=True, launch=True): """Inelegant for now, but lets you manually analyze every ABF in a folder.""" IN=INDEX(ABFfolder) if analyze: IN.analyzeAll() if convert: IN.convertImages()
def analyzeSingle(abfFname): """Reanalyze data for a single ABF. Also remakes child and parent html.""" assert os.path.exists(abfFname) and abfFname.endswith(".abf") ABFfolder,ABFfname=os.path.split(abfFname) abfID=os.path.splitext(ABFfname)[0] IN=INDEX(ABFfolder) IN.analyzeABF(abfID) IN.sca...
def scan(self): """ scan folder1 and folder2 into files1 and files2. since we are on windows, simplify things by making them all lowercase. this WILL cause problems on 'nix operating systems.If this is the case, just run a script to rename every file to all lowercase. """...
def convertImages(self): """ run this to turn all folder1 TIFs and JPGs into folder2 data. TIFs will be treated as micrographs and converted to JPG with enhanced contrast. JPGs will simply be copied over. """ # copy over JPGs (and such) exts=['.jpg','.png'] ...
def analyzeAll(self): """analyze every unanalyzed ABF in the folder.""" searchableData=str(self.files2) self.log.debug("considering analysis for %d ABFs",len(self.IDs)) for ID in self.IDs: if not ID+"_" in searchableData: self.log.debug("%s needs analysis",ID)...
def analyzeABF(self,ID): """ Analye a single ABF: make data, index it. If called directly, will delete all ID_data_ and recreate it. """ for fname in self.files2: if fname.startswith(ID+"_data_"): self.log.debug("deleting [%s]",fname) o...
def htmlFor(self,fname): """return appropriate HTML determined by file extension.""" if os.path.splitext(fname)[1].lower() in ['.jpg','.png']: html='<a href="%s"><img src="%s"></a>'%(fname,fname) if "_tif_" in fname: html=html.replace('<img ','<img class="datapic ...
def html_single_basic(self,abfID,launch=False,overwrite=False): """ generate a generic flat file html for an ABF parent. You could give this a single ABF ID, its parent ID, or a list of ABF IDs. If a child ABF is given, the parent will automatically be used. """ if type(a...
def html_single_plot(self,abfID,launch=False,overwrite=False): """create ID_plot.html of just intrinsic properties.""" if type(abfID) is str: abfID=[abfID] for thisABFid in cm.abfSort(abfID): parentID=cm.parent(self.groups,thisABFid) saveAs=os.path.abspath("%s...
def lowpass(data,filterSize=None): """ minimal complexity low-pass filtering. Filter size is how "wide" the filter will be. Sigma will be 1/10 of this filter width. If filter size isn't given, it will be 1/10 of the data size. """ if filterSize is None: filterSize=len(data)/10 ke...
def convolve(signal,kernel): """ This applies a kernel to a signal through convolution and returns the result. Some magic is done at the edges so the result doesn't apprach zero: 1. extend the signal's edges with len(kernel)/2 duplicated values 2. perform the convolution ('same' mode) ...
def timeit(timer=None): """simple timer. returns a time object, or a string.""" if timer is None: return time.time() else: took=time.time()-timer if took<1: return "%.02f ms"%(took*1000.0) elif took<60: return "%.02f s"%(took) else: ...
def list_move_to_front(l,value='other'): """if the value is in the list, move it to the front and return it.""" l=list(l) if value in l: l.remove(value) l.insert(0,value) return l
def list_move_to_back(l,value='other'): """if the value is in the list, move it to the back and return it.""" l=list(l) if value in l: l.remove(value) l.append(value) return l
def list_order_by(l,firstItems): """given a list and a list of items to be first, return the list in the same order except that it begins with each of the first items.""" l=list(l) for item in firstItems[::-1]: #backwards if item in l: l.remove(item) l.insert(0,item) ...
def abfSort(IDs): """ given a list of goofy ABF names, return it sorted intelligently. This places things like 16o01001 after 16901001. """ IDs=list(IDs) monO=[] monN=[] monD=[] good=[] for ID in IDs: if ID is None: continue if 'o' in ID: m...
def abfGroups(abfFolder): """ Given a folder path or list of files, return groups (dict) by cell. Rules which define parents (cells): * assume each cell has one or several ABFs * that cell can be labeled by its "ID" or "parent" ABF (first abf) * the ID is just the filename of the fi...
def abfGroupFiles(groups,folder): """ when given a dictionary where every key contains a list of IDs, replace the keys with the list of files matching those IDs. This is how you get a list of files belonging to each child for each parent. """ assert os.path.exists(folder) files=os.listdir(fo...
def parent(groups,ID): """given a groups dictionary and an ID, return its actual parent ID.""" if ID in groups.keys(): return ID # already a parent if not ID in groups.keys(): for actualParent in groups.keys(): if ID in groups[actualParent]: return actualParent # ...
def filesByType(fileList): """ given a list of files, return them as a dict sorted by type: * plot, tif, data, other """ features=["plot","tif","data","other","experiment"] files={} for feature in features: files[feature]=[] for fname in fileList: other=True f...
def userFolder(): """return the semi-temporary user folder""" #path=os.path.abspath(tempfile.gettempdir()+"/swhlab/") #don't use tempdir! it will get deleted easily. path=os.path.expanduser("~")+"/.swhlab/" # works on windows or linux # for me, path=r"C:\Users\swharden\.swhlab" if not os.path.ex...
def abfFname_Load(): """return the path of the last loaded ABF.""" fname=userFolder()+"/abfFname.ini" if os.path.exists(fname): abfFname=open(fname).read().strip() if os.path.exists(abfFname) or abfFname.endswith("_._"): return abfFname return os.path.abspath(os.sep)
def abfFname_Save(abfFname): """return the path of the last loaded ABF.""" fname=userFolder()+"/abfFname.ini" with open(fname,'w') as f: f.write(os.path.abspath(abfFname)) return
def gui_getFile(): """ Launch an ABF file selection file dialog. This is smart, and remembers (through reboots) where you last were. """ import tkinter as tk from tkinter import filedialog root = tk.Tk() # this is natively supported by python root.withdraw() # hide main window root.w...
def gui_getFolder(): """ Launch a folder selection dialog. This is smart, and remembers (through reboots) where you last were. """ import tkinter as tk from tkinter import filedialog root = tk.Tk() # this is natively supported by python root.withdraw() # hide main window root.wm_attr...
async def _try_catch_coro(emitter, event, listener, coro): """Coroutine wrapper to catch errors after async scheduling. Args: emitter (EventEmitter): The event emitter that is attempting to call a listener. event (str): The event that triggered the emitter. listener (async d...
def _check_limit(self, event): """Check if the listener limit is hit and warn if needed.""" if self.count(event) > self.max_listeners: warnings.warn( 'Too many listeners for event {}'.format(event), ResourceWarning, )
def add_listener(self, event, listener): """Bind a listener to a particular event. Args: event (str): The name of the event to listen for. This may be any string value. listener (def or async def): The callback to execute when the event fires. Thi...
def once(self, event, listener): """Add a listener that is only called once.""" self.emit('new_listener', event, listener) self._once[event].append(listener) self._check_limit(event) return self
def remove_listener(self, event, listener): """Remove a listener from the emitter. Args: event (str): The event name on which the listener is bound. listener: A reference to the same object given to add_listener. Returns: bool: True if a listener was removed...
def remove_all_listeners(self, event=None): """Remove all listeners, or those of the specified *event*. It's not a good idea to remove listeners that were added elsewhere in the code, especially when it's on an emitter that you didn't create (e.g. sockets or file streams). """ ...