Exemple #1
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    def test_Track_read(track):
        # test Track data format
        from etrack.io import trackio
        import os

        filebase = ''.join(
            chr(i) for i in np.random.randint(97, 122, size=(8, )))
        filename = '.'.join([filebase, 'h5'])
        with h5py.File(filename, 'a') as h5file:
            trackio.write_object_to_hdf5(track, h5file, 'track')
        with h5py.File(filename, 'r') as h5file:
            track2 = trackio.read_object_from_hdf5(h5file['track'])

        assert track2['is_modeled'] == track.is_modeled
        assert track2['pixel_size_um'] == track.pixel_size_um
        assert track2['noise_ev'] == track.noise_ev
        assert track2['label'] == track.label
        assert track2['energy_kev'] == track.energy_kev
        assert np.all(track2['image'] == track.image)

        assert track2['algorithms']['python HT v1.5']['alpha_deg'] == 120.5
        assert track2['algorithms']['python HT v1.5']['beta_deg'] == 43.5

        test_Track_from_pydict(track, track2)

        test_Track_from_hdf5()

        os.remove(filename)
Exemple #2
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def pyobjs_to_h5(g4tracks, pixnoise, filename, v):
    """
    Given the python object lists, write to HDF5 file at filename.
    """

    with h5py.File(filename, 'w', libver='latest', driver='core') as f:
        for ind in range(len(g4tracks)):
            pyobj_to_h5 = {}
            indstr = '{:05d}'.format(ind)
            g = f.create_group(indstr)

            # write g4track
            if g4tracks[ind]:
                filejob.vprint(
                    v, 3,
                    'Writing ' + str(ind) + ' g4track at ' + time.ctime())
                trackio.write_object_to_hdf5(g4tracks[ind],
                                             g,
                                             'g4track',
                                             pyobj_to_h5=pyobj_to_h5)

            # write each pixnoise
            for key, val in pixnoise.iteritems():
                filejob.vprint(
                    v, 4,
                    'Writing ' + str(ind) + ' ' + key + ' at ' + time.ctime())
                if isinstance(val[ind], trackdata.Track):
                    trackio.write_object_to_hdf5(val[ind],
                                                 g,
                                                 key,
                                                 pyobj_to_h5=pyobj_to_h5)
                else:
                    # track error code
                    t = g.create_group(key)
                    t.attrs['errorcode'] = val[ind]
Exemple #3
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    def test_Track_read(track):
        # test Track data format
        from etrack.io import trackio
        import os

        filebase = ''.join(
            chr(i) for i in np.random.randint(97, 122, size=(8,)))
        filename = '.'.join([filebase, 'h5'])
        with h5py.File(filename, 'a') as h5file:
            trackio.write_object_to_hdf5(
                track, h5file, 'track')
        with h5py.File(filename, 'r') as h5file:
            track2 = trackio.read_object_from_hdf5(
                h5file['track'])

        assert track2['is_modeled'] == track.is_modeled
        assert track2['pixel_size_um'] == track.pixel_size_um
        assert track2['noise_ev'] == track.noise_ev
        assert track2['label'] == track.label
        assert track2['energy_kev'] == track.energy_kev
        assert np.all(track2['image'] == track.image)

        assert track2['algorithms']['python HT v1.5']['alpha_deg'] == 120.5
        assert track2['algorithms']['python HT v1.5']['beta_deg'] == 43.5

        test_Track_from_pydict(track, track2)

        test_Track_from_hdf5()

        os.remove(filename)
Exemple #4
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def pyobjs_to_h5(g4tracks, pixnoise, filename, v):
    """
    Given the python object lists, write to HDF5 file at filename.
    """

    with h5py.File(filename, "w", libver="latest", driver="core") as f:
        for ind in range(len(g4tracks)):
            pyobj_to_h5 = {}
            indstr = "{:05d}".format(ind)
            g = f.create_group(indstr)

            # write g4track
            if g4tracks[ind]:
                filejob.vprint(v, 3, "Writing " + str(ind) + " g4track at " + time.ctime())
                trackio.write_object_to_hdf5(g4tracks[ind], g, "g4track", pyobj_to_h5=pyobj_to_h5)

            # write each pixnoise
            for key, val in pixnoise.iteritems():
                filejob.vprint(v, 4, "Writing " + str(ind) + " " + key + " at " + time.ctime())
                if isinstance(val[ind], trackdata.Track):
                    trackio.write_object_to_hdf5(val[ind], g, key, pyobj_to_h5=pyobj_to_h5)
                else:
                    # track error code
                    t = g.create_group(key)
                    t.attrs["errorcode"] = val[ind]
Exemple #5
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def classify_etc(loadfile, savefile, v):
    """
    1. Moments algorithm
    2. HybridTrack algorithm
    3. Classify
    """

    progressflag = not file_vars()[0]

    pn = 'pix10_5noise15'
    HTname = 'python HT v1.52'
    MTname = 'moments v1.0'

    vprint(v, 1, 'Starting {} at {} with {}% mem usage'.format(
        loadfile, time.ctime(), psutil.virtual_memory().percent))

    pyobj_to_h5 = {}

    try:
        with h5py.File(loadfile, 'a', driver='core') as f, h5py.File(
                savefile, 'a', driver='core') as h5save:
            #
            n = 0
            if progressflag:
                pbar = progressbar.ProgressBar(
                    widgets=[progressbar.Percentage(), ' ',
                             progressbar.Bar(), ' ',
                             progressbar.ETA()], maxval=len(f))
                pbar.start()

            keylist = f.keys()
            keylist.sort()
            for ind in keylist:
                vprint(v, 3, 'Beginning track {} in {}'.format(ind, loadfile))
                if int(ind) % 50 == 0:
                    vprint(v, 2,
                           'Beginning track {} in {}'.format(ind, loadfile))

                # evt is for the G4Track object
                evt = f[ind]
                # shouldn't get a KeyError because we are looping over ind

                # trk is for the Track object
                try:
                    trk = evt[pn]
                except KeyError:
                    vprint(v, 1,
                           '**Missing key {} in {}{}, skipping'.format(
                               pn, loadfile, evt.name))
                    continue

                trkpath = ind + '/' + pn
                errorcode = 0
                n += 1

                if n > 50:
                    # testing
                    # vprint(v, 1, 'Finished 50 files, exiting')
                    # break
                    pass

                # load G4Track
                vprint(v, 3, 'Loading G4Track {} in {}'.format(ind, loadfile))
                try:
                    this_g4track = G4Track.from_dth5(evt)
                except trackio.InterfaceError:
                    vprint(v, 2, 'InterfaceError in G4Track at {}, {}'.format(
                        loadfile, ind))
                    continue

                # load Track
                vprint(v, 3, 'Loading Track {} in {}'.format(ind, loadfile))
                try:
                    this_track = Track.from_dth5(trk, g4track=this_g4track)
                except trackio.InterfaceError:
                    vprint(v, 2, 'InterfaceError in Track at {}, {}'.format(
                        loadfile, ind))
                    continue

                # check for error codes - Track.from_dth5 may return an int
                if isinstance(this_track, int):
                    this_save = h5save.create_group(trkpath)
                    this_save.attrs.create(
                        'errorcode', this_track, shape=np.shape(this_track))
                    continue

                # run moments algorithm
                vprint(v, 3, 'Running moments on track {} in {}'.format(
                    ind, loadfile))
                try:
                    mom = tm.MomentsReconstruction(this_track.image)
                    mom.reconstruct()
                except ht.NoEndsFound:
                    mom.alpha = None
                    errorcode = 4
                    this_save = h5save.create_group('mom_' + trkpath)
                    this_save.attrs.create(
                        'errorcode', errorcode, shape=np.shape(errorcode))
                else:
                    # write into savefile
                    trackio.write_object_to_hdf5(
                        mom, h5save, 'mom_' + trkpath, pyobj_to_h5=pyobj_to_h5)
                # write into track object
                if mom.alpha:
                    this_track.add_algorithm(
                        MTname,
                        alpha_deg=mom.alpha * 180 / np.pi,
                        beta_deg=np.nan, info=None)
                else:
                    this_track.add_algorithm(
                        MTname,
                        alpha_deg=np.nan,
                        beta_deg=np.nan, info=None)

                # run HT algorithm (v1.52)
                vprint(v, 3, 'Running HT on track {} in {}'.format(
                    ind, loadfile))
                try:
                    _, HTinfo = ht.reconstruct(this_track)
                except (ht.InfiniteLoop, ht.NoEndsFound):
                    # write empty into track object
                    this_track.add_algorithm(
                        HTname,
                        alpha_deg=np.nan,
                        beta_deg=np.nan,
                        info=None)
                else:
                    # trim memory usage
                    if hasattr(HTinfo, 'ridge'):
                        if HTinfo.ridge:
                            for ridgept in HTinfo.ridge:
                                ridgept.cuts = None
                                ridgept.best_cut = None
                    # write into track object
                    this_track.add_algorithm(
                        HTname,
                        alpha_deg=HTinfo.alpha_deg,
                        beta_deg=HTinfo.beta_deg,
                        info=HTinfo)

                # write py HDF5 format into savefile (including alg outputs)
                try:
                    trackio.write_object_to_hdf5(
                        this_track, h5save, trkpath,
                        pyobj_to_h5=pyobj_to_h5)
                except trackio.InterfaceError:
                    vprint(v, 1, 'InterfaceError writing to file at ' +
                           '{}, {}'.format(savefile, ind))
                    continue

                # run classifier
                vprint(v, 3, 'Running MC classifier on track {} in {}'.format(
                    ind, loadfile))
                classifier = cl.Classifier(this_track.g4track)
                try:
                    classifier.mc_classify()
                except cl.TrackTooShortError:
                    classifier.error = 'TrackTooShortError'
                else:
                    vprint(v, 3,
                           'Running ends classifier on track {} in {}'.format(
                               ind, loadfile))
                    try:
                        classifier.end_classify(this_track, mom=mom)
                    except tp.G4TrackTooBigError:
                        classifier.error = 'G4TrackTooBigError'
                    except cl.NoEnds:
                        classifier.error = 'NoEnds'
                # write into savefile
                vprint(v, 3, 'Writing classifier into {} for track {}'.format(
                    savefile, ind))
                trackio.write_object_to_hdf5(
                    classifier, h5save, 'cl_' + trkpath,
                    pyobj_to_h5=pyobj_to_h5)

                if progressflag:
                    pbar.update(n)
            if progressflag:
                pbar.finish()
        # f gets closed here
    except NotImplementedError:
        pass
Exemple #6
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def run_main():
    serverflag = True
    doneflag = False  # only take files that have an associated done file

    if serverflag:
        loadpath = '/global/home/users/bcplimley/multi_angle/HTbatch01_AR151/'
        savepath = loadpath
    else:
        loadpath = '/media/plimley/TEAM 7B/HTbatch01_AR/'
        savepath = loadpath

    loadglob = 'MultiAngle_HT_*_*_AR.h5'
    savename = 'compile_AR_' + str(int(time.time())) + '.h5'
    doneglob = 'done_MultiAngle_HT_*_*_AR.h5'

    if doneflag:
        flist = glob.glob(os.path.join(loadpath, doneglob))
        done2load = get_filename_function(doneglob, loadglob)
    else:
        flist = glob.glob(os.path.join(loadpath, loadglob))
    print('flist contains {} files'.format(str(len(flist))))

    pnlist = [
        'pix2_5noise0',
        'pix5noise0',
        'pix5noise15',
        'pix10_5noise0',
        'pix10_5noise15',
        'pix10_5noise20',
        'pix10_5noise50',
        'pix10_5noise100',
        'pix10_5noise200',
        'pix10_5noise500',
        'pix10_5noise1000',
        'pix10_5noise2000',
        'pix20noise0',
        'pix40noise0',
    ]
    alglist = [
        'python HT v1.52',
        'python HT v1.52b',
        'python HT v1.52c',
        'python HT v1.52d',
    ]

    AR = {}
    for fname in flist:
        if doneflag:
            donename = os.path.split(fname)[-1]
            loadname = done2load(donename)
            loadfile = os.path.join(loadpath, loadname)
        else:
            loadfile = fname
            loadname = fname

        try:
            with h5py.File(loadfile, 'r') as h5f:
                for pn in pnlist:
                    if pn not in AR:
                        AR[pn] = {}
                    for alg in alglist:
                        try:
                            this_AR = evaluation.AlgorithmResults.from_hdf5(
                                h5f[pn][alg])
                        except KeyError:
                            # happens once somewhere
                            print('KeyError on {} - {} - {}'.format(
                                loadname, pn, alg))
                            continue
                        try:
                            AR[pn][alg] += this_AR
                        except KeyError:
                            AR[pn][alg] = this_AR
        except IOError:
            print('IOError on {}; skipping'.format(loadfile))

    print('saving to {}'.format(os.path.join(savepath, savename)))
    with h5py.File(os.path.join(savepath, savename), 'w') as fsave:
        for pn in pnlist:
            fsave.create_group(pn)
            for alg in alglist:
                AR[pn][alg].add_default_uncertainties()
                trackio.write_object_to_hdf5(AR[pn][alg], fsave[pn], alg)
Exemple #7
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def pyml_run_algs(loadfile, savefile, v):

    progressflag = False     # turn off for parallel

    pnlist = [
        'pix2_5noise0',
        'pix5noise0',
        'pix5noise15',
        'pix10_5noise0',
        'pix10_5noise15',
        'pix10_5noise20',
        'pix10_5noise50',
        'pix10_5noise100',
        'pix10_5noise200',
        'pix10_5noise500',
        'pix10_5noise1000',
        'pix10_5noise2000',
        'pix20noise0',
        'pix40noise0',
    ]
    alglist = {
        'python HT v1.52': ht,
        # 'python HT v1.52a': ht_a,
        # 1.52a causes RuntimeWarning and possibly breaks something more...
        'python HT v1.52b': ht_b,
        'python HT v1.52c': ht_c,
        'python HT v1.52d': ht_d,
    }
    tracklist = {}
    AR = {}
    for pnname in pnlist:
        tracklist[pnname] = []
        AR[pnname] = {}
        for algname in alglist.keys():
            AR[pnname][algname] = []

    vprint(v, 1, 'Starting {} at {} with {}% mem usage'.format(
        loadfile, time.ctime(), psutil.virtual_memory().percent))
    try:
        with h5py.File(loadfile, 'a', driver='core') as h5load:
            filename = h5load.filename
            n = 0
            if progressflag:
                pbar = progressbar.ProgressBar(
                    widgets=[progressbar.Percentage(), ' ',
                             progressbar.Bar(), ' ',
                             progressbar.ETA()], maxval=len(h5load))
                pbar.start()

            keylist = h5load.keys()
            keylist.sort()
            for ind in keylist:
                if int(ind) % 10 == 0:
                    vprint(v, 2, '    Running {} #{} at {}'.format(
                        loadfile, ind, time.ctime()))
                trk = h5load[ind]
                h5_to_pydict = {}
                pydict_to_pyobj = {}
                pyobj_to_h5 = {}

                n += 1
                if n > 50:
                    # pdb.set_trace()
                    # continue  # TODO temp!
                    pass

                for pnname in pnlist:
                    try:
                        pn = trk[pnname]
                    except KeyError:
                        vprint(v, 1,
                               '**Missing key {} in {}{}, skipping'.format(
                                   pnname, loadfile, trk.name))
                        continue
                    vprint(v, 3, 'Running {}{} at {}'.format(
                        loadfile, pn.name, time.ctime()))
                    # load track
                    try:
                        this_track = trackdata.Track.from_hdf5(
                            pn,
                            h5_to_pydict=h5_to_pydict,
                            pydict_to_pyobj=pydict_to_pyobj)
                    except trackio.InterfaceError:
                        vprint(v, 2, 'InterfaceError at {}{}'.format(
                            loadfile, pn.name))
                        continue
                    tracklist[pnname].append(this_track)
                    # each algorithm version
                    for algname, algfunc in alglist.items():
                        vprint(v, 4, 'Running alg {} at {}'.format(
                            algname, time.ctime()))
                        # check for result
                        if algname not in this_track.algorithms:
                            # run algorithm
                            try:
                                _, HTinfo = algfunc.reconstruct(this_track)
                            except algfunc.InfiniteLoop:
                                continue
                            except algfunc.NoEndsFound:
                                continue
                            # trim memory usage!
                            if hasattr(HTinfo, 'ridge'):
                                if HTinfo.ridge:
                                    for ridgept in HTinfo.ridge:
                                        ridgept.cuts = None
                                        ridgept.best_cut = None
                            # write into track object
                            try:
                                this_track.add_algorithm(
                                    algname,
                                    alpha_deg=HTinfo.alpha_deg,
                                    beta_deg=HTinfo.beta_deg,
                                    info=HTinfo)
                                # write into HDF5
                                trackio.write_object_to_hdf5(
                                    this_track.algorithms[algname],
                                    pn['algorithms'], algname,
                                    pyobj_to_h5=pyobj_to_h5)
                            except trackdata.InputError:
                                # already has this algorithm
                                pass

                if progressflag:
                    pbar.update(n)
            if progressflag:
                pbar.finish()
            # h5load gets closed
            vprint(
                v, 1.5,
                '\n  Finished loading {} at {} with {}% mem usage'.format(
                    loadfile, time.ctime(), psutil.virtual_memory().percent))
    except IOError:
        vprint(v, 1, 'IOError: Unable to open file (I think) for {}'.format(
            loadfile))
        return None

    # AlgorithmResults objects
    alglist2 = alglist.keys()  # + ['matlab HT v1.5']
    for pnname in pnlist:
        for algname in alglist2:
            this_AR = evaluation.AlgorithmResults.from_track_list(
                tracklist[pnname], alg_name=algname, filename=filename)
            AR[pnname][algname] = this_AR
    vprint(v, 2, '\n  Created AR objects for {} at {}'.format(
        loadfile, time.ctime()))

    # write to savefile
    try:
        with h5py.File(savefile, 'w', driver='core') as h5save:
            for pnname, AR_pn in AR.items():
                pngroup = h5save.create_group(pnname)
                for algname, this_AR in AR_pn.items():
                    trackio.write_object_to_hdf5(this_AR, pngroup, algname)
        vprint(v, 1.5,
               'Finished saving {} at {}'.format(savefile, time.ctime()))
    except IOError:
        vprint(v, 1, 'IOError: Unable to create file (I think) for {}'.format(
            savefile))

    return None
Exemple #8
0
def pyml_run_algs(loadfile, savefile, v):

    progressflag = False  # turn off for parallel

    pnlist = [
        'pix2_5noise0',
        'pix5noise0',
        'pix5noise15',
        'pix10_5noise0',
        'pix10_5noise15',
        'pix10_5noise20',
        'pix10_5noise50',
        'pix10_5noise100',
        'pix10_5noise200',
        'pix10_5noise500',
        'pix10_5noise1000',
        'pix10_5noise2000',
        'pix20noise0',
        'pix40noise0',
    ]
    alglist = {
        'python HT v1.52': ht,
        # 'python HT v1.52a': ht_a,
        # 1.52a causes RuntimeWarning and possibly breaks something more...
        'python HT v1.52b': ht_b,
        'python HT v1.52c': ht_c,
        'python HT v1.52d': ht_d,
    }
    tracklist = {}
    AR = {}
    for pnname in pnlist:
        tracklist[pnname] = []
        AR[pnname] = {}
        for algname in alglist.keys():
            AR[pnname][algname] = []

    vprint(
        v, 1, 'Starting {} at {} with {}% mem usage'.format(
            loadfile, time.ctime(),
            psutil.virtual_memory().percent))
    try:
        with h5py.File(loadfile, 'a', driver='core') as h5load:
            filename = h5load.filename
            n = 0
            if progressflag:
                pbar = progressbar.ProgressBar(widgets=[
                    progressbar.Percentage(), ' ',
                    progressbar.Bar(), ' ',
                    progressbar.ETA()
                ],
                                               maxval=len(h5load))
                pbar.start()

            keylist = h5load.keys()
            keylist.sort()
            for ind in keylist:
                if int(ind) % 10 == 0:
                    vprint(
                        v, 2, '    Running {} #{} at {}'.format(
                            loadfile, ind, time.ctime()))
                trk = h5load[ind]
                h5_to_pydict = {}
                pydict_to_pyobj = {}
                pyobj_to_h5 = {}

                n += 1
                if n > 50:
                    # pdb.set_trace()
                    # continue  # TODO temp!
                    pass

                for pnname in pnlist:
                    try:
                        pn = trk[pnname]
                    except KeyError:
                        vprint(
                            v, 1, '**Missing key {} in {}{}, skipping'.format(
                                pnname, loadfile, trk.name))
                        continue
                    vprint(
                        v, 3,
                        'Running {}{} at {}'.format(loadfile, pn.name,
                                                    time.ctime()))
                    # load track
                    try:
                        this_track = trackdata.Track.from_hdf5(
                            pn,
                            h5_to_pydict=h5_to_pydict,
                            pydict_to_pyobj=pydict_to_pyobj)
                    except trackio.InterfaceError:
                        vprint(
                            v, 2,
                            'InterfaceError at {}{}'.format(loadfile, pn.name))
                        continue
                    tracklist[pnname].append(this_track)
                    # each algorithm version
                    for algname, algfunc in alglist.items():
                        vprint(
                            v, 4, 'Running alg {} at {}'.format(
                                algname, time.ctime()))
                        # check for result
                        if algname not in this_track.algorithms:
                            # run algorithm
                            try:
                                _, HTinfo = algfunc.reconstruct(this_track)
                            except algfunc.InfiniteLoop:
                                continue
                            except algfunc.NoEndsFound:
                                continue
                            # trim memory usage!
                            if hasattr(HTinfo, 'ridge'):
                                if HTinfo.ridge:
                                    for ridgept in HTinfo.ridge:
                                        ridgept.cuts = None
                                        ridgept.best_cut = None
                            # write into track object
                            try:
                                this_track.add_algorithm(
                                    algname,
                                    alpha_deg=HTinfo.alpha_deg,
                                    beta_deg=HTinfo.beta_deg,
                                    info=HTinfo)
                                # write into HDF5
                                trackio.write_object_to_hdf5(
                                    this_track.algorithms[algname],
                                    pn['algorithms'],
                                    algname,
                                    pyobj_to_h5=pyobj_to_h5)
                            except trackdata.InputError:
                                # already has this algorithm
                                pass

                if progressflag:
                    pbar.update(n)
            if progressflag:
                pbar.finish()
            # h5load gets closed
            vprint(
                v, 1.5,
                '\n  Finished loading {} at {} with {}% mem usage'.format(
                    loadfile, time.ctime(),
                    psutil.virtual_memory().percent))
    except IOError:
        vprint(
            v, 1,
            'IOError: Unable to open file (I think) for {}'.format(loadfile))
        return None

    # AlgorithmResults objects
    alglist2 = alglist.keys()  # + ['matlab HT v1.5']
    for pnname in pnlist:
        for algname in alglist2:
            this_AR = evaluation.AlgorithmResults.from_track_list(
                tracklist[pnname], alg_name=algname, filename=filename)
            AR[pnname][algname] = this_AR
    vprint(
        v, 2,
        '\n  Created AR objects for {} at {}'.format(loadfile, time.ctime()))

    # write to savefile
    try:
        with h5py.File(savefile, 'w', driver='core') as h5save:
            for pnname, AR_pn in AR.items():
                pngroup = h5save.create_group(pnname)
                for algname, this_AR in AR_pn.items():
                    trackio.write_object_to_hdf5(this_AR, pngroup, algname)
        vprint(v, 1.5,
               'Finished saving {} at {}'.format(savefile, time.ctime()))
    except IOError:
        vprint(
            v, 1,
            'IOError: Unable to create file (I think) for {}'.format(savefile))

    return None
Exemple #9
0
def run_main():
    serverflag = True
    doneflag = False     # only take files that have an associated done file

    if serverflag:
        loadpath = '/global/home/users/bcplimley/multi_angle/HTbatch01_AR151/'
        savepath = loadpath
    else:
        loadpath = '/media/plimley/TEAM 7B/HTbatch01_AR/'
        savepath = loadpath

    loadglob = 'MultiAngle_HT_*_*_AR.h5'
    savename = 'compile_AR_' + str(int(time.time())) + '.h5'
    doneglob = 'done_MultiAngle_HT_*_*_AR.h5'

    if doneflag:
        flist = glob.glob(os.path.join(loadpath, doneglob))
        done2load = get_filename_function(doneglob, loadglob)
    else:
        flist = glob.glob(os.path.join(loadpath, loadglob))
    print('flist contains {} files'.format(str(len(flist))))

    pnlist = [
        'pix2_5noise0',
        'pix5noise0',
        'pix5noise15',
        'pix10_5noise0',
        'pix10_5noise15',
        'pix10_5noise20',
        'pix10_5noise50',
        'pix10_5noise100',
        'pix10_5noise200',
        'pix10_5noise500',
        'pix10_5noise1000',
        'pix10_5noise2000',
        'pix20noise0',
        'pix40noise0',
    ]
    alglist = [
        'python HT v1.52',
        'python HT v1.52b',
        'python HT v1.52c',
        'python HT v1.52d',
    ]

    AR = {}
    for fname in flist:
        if doneflag:
            donename = os.path.split(fname)[-1]
            loadname = done2load(donename)
            loadfile = os.path.join(loadpath, loadname)
        else:
            loadfile = fname
            loadname = fname

        try:
            with h5py.File(loadfile, 'r') as h5f:
                for pn in pnlist:
                    if pn not in AR:
                        AR[pn] = {}
                    for alg in alglist:
                        try:
                            this_AR = evaluation.AlgorithmResults.from_hdf5(
                                h5f[pn][alg])
                        except KeyError:
                            # happens once somewhere
                            print('KeyError on {} - {} - {}'.format(
                                loadname, pn, alg))
                            continue
                        try:
                            AR[pn][alg] += this_AR
                        except KeyError:
                            AR[pn][alg] = this_AR
        except IOError:
            print('IOError on {}; skipping'.format(loadfile))

    print('saving to {}'.format(os.path.join(savepath, savename)))
    with h5py.File(os.path.join(savepath, savename), 'w') as fsave:
        for pn in pnlist:
            fsave.create_group(pn)
            for alg in alglist:
                AR[pn][alg].add_default_uncertainties()
                trackio.write_object_to_hdf5(AR[pn][alg], fsave[pn], alg)