Beispiel #1
0
def import_data(ID, setup='omicron'):
    db = Cinfdata(setup, use_caching=True)
    data = db.get_data(ID)
    try:
        data[:,0] = data[:,0]/1000
    except:
        meta = db.get_metadata(ID)
        print('"{}" data for ID {} is empty and set to "None"'.format(meta['mass_label'], ID))
        data = None
    return data
Beispiel #2
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def import_data(ID, setup='omicron'):
    db = Cinfdata(setup, use_caching=True)
    data = db.get_data(ID)
    try:
        data[:,0] = data[:,0]/1000
    except:
        meta = db.get_metadata(ID)
        print('"{}" data for ID {} is empty and set to "None"'.format(meta['mass_label'], ID))
        data = None
    return data
Beispiel #3
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def download_cinfdata_set(
    setup="sniffer", group_id=None, grouping_column=None, **kwargs
):

    if grouping_column is None:
        grouping_column, group_id = kwargs.popitem()

    from .Combining import synchronize

    try:
        from cinfdata import Cinfdata
    except ImportError:
        print(
            "the cinfdata module must be on your python path. It's here: \n"
            + "https://github.com/CINF/cinf_database/blob/master/cinfdata.py"
        )

    try:
        cinfd = Cinfdata(
            setup,
            grouping_column=grouping_column,
            allow_wildcards=True,
            label_column="mass_label",
        )
    except:
        raise  # untill I know exactly which error I'm trying to catch.
        print("couldn't connect. You should run gstm")
        # os.system('gstm')
        raise RuntimeError("Couldn't connect to cinfdata!")

    # obj = cinfd.get_metadata_group('2018-03-30 14:13:17')

    # all_datasets = cinfd.get_metadata_group('%')
    # the_list = [(ID, d['time'], d['comment']) for ID, d in all_datasets.items()]
    # print(the_list)

    obj = cinfd.get_metadata_group(group_id)
    # print(str(obj)) #

    idlists = {}  # keys will be time as string. values will be corresponding id's

    for key, value in obj.items():
        # label = value['mass_label']
        # print(label)
        timestamp = str(value["time"])
        if timestamp not in idlists:
            idlists[timestamp] = []
        idlists[timestamp] += [value["id"]]

    datasets = {}
    for timestamp, idlist in idlists.items():

        if len(idlist) == 0:
            print("No data associated with timestamp '" + timestamp + "'.")
            continue

        dataset = {"title": timestamp, "data_type": "MS"}

        metadatas = dict([(i, cinfd.get_metadata(i)) for i in idlist])

        unixtimes = [metadatas[i]["unixtime"] for i in idlist]
        if len(set(unixtimes)) > 1:
            msg = "unix times don't match for timestamp '" + timestamp + "'!"
            raise ValueError(msg)

        dataset["tstamp"] = unixtimes[0]
        dataset["timestamp"] = metadatas[idlist[0]]["time"].strftime("%H:%M:%S")

        labels = [metadatas[i]["mass_label"] for i in idlist]
        if "Mass Scan" in labels:
            dataset["scan_type"] = "mass"
        else:
            dataset["scan_type"] = "time"

        dataset["data_cols"] = set()
        dataset["timecols"] = {}
        for i in idlist:  # avoiding id since it's got a builtin meaning
            data = cinfd.get_data(i)
            label = metadatas[i]["mass_label"]
            if len(data.shape) == 1:
                dataset[label] = data
                dataset["data_cols"].add(label)
            elif data.shape[1] == 2:
                x = data[:, 0]
                y = data[:, 1]
                x_label = label + "-x"
                y_label = label + "-y"
                dataset["timecols"][y_label] = x_label  # Fixed 20B26!!!
                dataset[x_label] = x * 1e-3  # cinfdata saves time in ms!!!
                dataset[y_label] = y

                dataset["data_cols"].add(x_label)
                dataset["data_cols"].add(y_label)

        datasets[timestamp] = dataset

    timescans = [
        dataset for dataset in datasets.values() if dataset["scan_type"] == "time"
    ]

    combined = synchronize(timescans, t_zero="first")

    return combined
Beispiel #4
0
import datetime
import numpy as np
from cinfdata import Cinfdata

DATA_CHECKSUM = 12525.0000008
METADATA = {
    'comment': '', 'tof_liner_voltage': None, 'tof_iterations': None,
    'timestep': 0.1, 'id': 5417L, 'preamp_range': -7, 'tof_pulse_width': None,
    'pre_wait_time': None, 'tof_ion_energy': None, 'tof_R2_voltage': None,
    'mass_label': None, 'tof_R1_voltage': None, 'sem_voltage': 1798.83,
    u'unixtime': 1464261944L, 'type': 4L, 'pass_energy': None,
    'time': datetime.datetime(2016, 5, 26, 13, 25, 44),
    'sample_temperature': None, 'tof_focus_voltage': None,
    'tof_pulse_voltage': None, 'tof_emission_current': None,
    'tof_deflection_voltage': None, 'tof_p1_2': None, 'tof_p1_0': None,
    'tof_p1_1': None, 'tof_lens_E': None, 'tof_lens_D': None,
    'tof_lens_A': None, 'tof_lens_C': None, 'tof_lens_B': None
}

cinfdata = Cinfdata('tof', use_caching=True)
# Get from database
assert np.isclose(cinfdata.get_data(5417).sum(), DATA_CHECKSUM)
assert cinfdata.get_metadata(5417) == METADATA
print('Test database OK')
# And now fetch from cache
assert np.isclose(cinfdata.get_data(5417).sum(), DATA_CHECKSUM)
assert cinfdata.get_metadata(5417) == METADATA
print('Test cache OK')

from cinfdata import Cinfdata

db = Cinfdata('stm312', use_caching=True)
spectrum = db.get_data(6688)
metadata = db.get_metadata(6688)
Beispiel #6
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    'tof_R1_voltage': None,
    'sem_voltage': 1798.83,
    u'unixtime': 1464261944L,
    'type': 4L,
    'pass_energy': None,
    'time': datetime.datetime(2016, 5, 26, 13, 25, 44),
    'sample_temperature': None,
    'tof_focus_voltage': None,
    'tof_pulse_voltage': None,
    'tof_emission_current': None,
    'tof_deflection_voltage': None,
    'tof_p1_2': None,
    'tof_p1_0': None,
    'tof_p1_1': None,
    'tof_lens_E': None,
    'tof_lens_D': None,
    'tof_lens_A': None,
    'tof_lens_C': None,
    'tof_lens_B': None
}

cinfdata = Cinfdata('tof', use_caching=True)
# Get from database
assert np.isclose(cinfdata.get_data(5417).sum(), DATA_CHECKSUM)
assert cinfdata.get_metadata(5417) == METADATA
print('Test database OK')
# And now fetch from cache
assert np.isclose(cinfdata.get_data(5417).sum(), DATA_CHECKSUM)
assert cinfdata.get_metadata(5417) == METADATA
print('Test cache OK')
Beispiel #7
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def download_cinfdata_set(setup='sniffer',
                          group_id=None,
                          grouping_column=None,
                          **kwargs):

    if grouping_column is None:
        grouping_column, group_id = kwargs.popitem()

    from .Combining import synchronize

    try:
        from cinfdata import Cinfdata
    except ImportError:
        print(
            'the cinfdata module must be on your python path. It\'s here: \n' +
            'https://github.com/CINF/cinf_database/blob/master/cinfdata.py')

    try:
        cinfd = Cinfdata(setup,
                         grouping_column=grouping_column,
                         allow_wildcards=True,
                         label_column='mass_label')
    except:
        raise  #untill I know exactly which error I'm trying to catch.
        print('couldn\'t connect. You should run gstm')
        #os.system('gstm')
        raise RuntimeError('Couldn\'t connect to cinfdata!')

    #obj = cinfd.get_metadata_group('2018-03-30 14:13:17')

    #all_datasets = cinfd.get_metadata_group('%')
    #the_list = [(ID, d['time'], d['comment']) for ID, d in all_datasets.items()]
    #print(the_list)

    obj = cinfd.get_metadata_group(group_id)
    #print(str(obj)) #

    idlists = {
    }  # keys will be time as string. values will be corresponding id's

    for key, value in obj.items():
        #label = value['mass_label']
        #print(label)
        timestamp = str(value['time'])
        if timestamp not in idlists:
            idlists[timestamp] = []
        idlists[timestamp] += [value['id']]

    datasets = {}
    for timestamp, idlist in idlists.items():

        if len(idlist) == 0:
            print('No data associated with timestamp \'' + timestamp + '\'.')
            continue

        dataset = {'title': timestamp, 'data_type': 'MS'}

        metadatas = dict([(i, cinfd.get_metadata(i)) for i in idlist])

        unixtimes = [metadatas[i]['unixtime'] for i in idlist]
        if len(set(unixtimes)) > 1:
            msg = 'unix times don\'t match for timestamp \'' + timestamp + '\'!'
            raise ValueError(msg)

        dataset['tstamp'] = unixtimes[0]
        dataset['timestamp'] = metadatas[idlist[0]]['time'].strftime(
            '%H:%M:%S')

        labels = [metadatas[i]['mass_label'] for i in idlist]
        if 'Mass Scan' in labels:
            dataset['scan_type'] = 'mass'
        else:
            dataset['scan_type'] = 'time'

        dataset['data_cols'] = set()
        dataset['timecols'] = {}
        for i in idlist:  #avoiding id since it's got a builtin meaning
            data = cinfd.get_data(i)
            label = metadatas[i]['mass_label']
            if len(data.shape) == 1:
                dataset[label] = data
                dataset['data_cols'].add(label)
            elif data.shape[1] == 2:
                x = data[:, 0]
                y = data[:, 1]
                x_label = label + '-x'
                y_label = label + '-y'
                dataset['timecols'][x_label] = y_label
                dataset[x_label] = x * 1e-3  # cinfdata saves time in ms!!!
                dataset[y_label] = y

                dataset['data_cols'].add(x_label)
                dataset['data_cols'].add(y_label)

        datasets[timestamp] = dataset

    timescans = [
        dataset for dataset in datasets.values()
        if dataset['scan_type'] == 'time'
    ]

    combined = synchronize(timescans, t_zero='first')

    return combined
Beispiel #8
0
from cinfdata import Cinfdata
from matplotlib import pyplot as plt

db = Cinfdata('stm312')
spectrum = db.get_data(6688)
metadata = db.get_metadata(6688)

plt.plot(spectrum[:, 0], spectrum[:, 1])
plt.title(metadata['Comment'])
plt.show()
Beispiel #9
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    #ID = 17601 # SA1
    #ID = 17585 # SA2
    ID = 14273  # 70% 6nm Pt
    STRING = '\
TARGET=5.0;\
MODEL=NP;\
SA_DENSITY=1.58426e19;\
PARTICLE_DIAMETER=6.0;\
APERTURE_DIAMETER=12.41;\
FIRST_LIMIT=20;\
SENSITIVITY_LIMIT=.7;SENSITIVITY_FILTER=1.;\
TIME=[];\
DEBUG=False'

    try:
        SESSION = IntegrateCurrent(STRING, db.get_data(ID), plot=True)
        SESSION.integrate()
        if SESSION.plot:
            limits = SESSION.ax2.axis()
            if SESSION.debugging:
                for ax in [
                        SESSION.dbg0, SESSION.dbg1, SESSION.dbg2, SESSION.ax1
                ]:
                    l1, l2, l3, l4 = ax.axis()
                    ax.axis([limits[0], limits[1], l3, l4])
            SESSION.plt.show()
    except:
        print(
            '***\nSomething is wrong: Check input parameters or try debugging mode!!\n***'
        )
        limits = SESSION.ax2.axis()
Beispiel #10
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settings = {
    #9489: 220,
    #9494: 400,
    #9504: 1500,
    #9507: 800,
    #9509: 1000,
    #9512: 600,
    #9516: 1000,
    #9518: 500,
    #9527: 600,
    9545: 350,
}

db = Cinfdata('dummy', use_caching=False)
for ID, LEVEL in settings.items():
    data = db.get_data(ID)
    time, signal = data[:, 0], data[:, 1]

    smooth = ct.smooth(signal)
    diff = np.abs(np.diff(signal-smooth))

    index = np.where(diff > LEVEL)[0] + 1
    i = np.where(time > 0)[0]
    
    if mode in ['test', 'plot']:
        plt.title(str(ID))
        plt.plot(data[:, 0], data[:, 1], 'b-', label='Raw data')
        plt.plot(time[index], signal[index], 'mo', markerfacecolor='w')

    index = [x for x in i if x not in index]
    if mode == 'plot':
Beispiel #11
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    #import rcparam
    from cinfdata import Cinfdata
    db = Cinfdata('omicron', use_caching=False)  # pylint: disable=invalid-name
    ID = 15372
    STRING = '\
TARGET=5.0;\
MODEL=NP;\
SA_DENSITY=1;\
PARTICLE_DIAMETER=5.0;\
APERTURE_DIAMETER=4.5;\
FIRST_LIMIT=10.8;\
SENSITIVITY_LIMIT=1.;SENSITIVITY_FILTER=1.;\
TIME=[]'

    try:
        SESSION = IntegrateCurrent(STRING, db.get_data(ID))
        SESSION.integrate()
        if SESSION.plot:
            SESSION.plt.show()
    except:
        print(
            '***\nSomething is wrong: Check input parameters or try debugging mode!!\n***'
        )
        SESSION.plt.show()
        raise
    # for 9x9 raster pattern: ap_dia ~ 12.4 mm (120.8 mm2 ~ 11x11 mm)
    # for 5x5 raster pattern: ap_dia ~ 6.7 mm (35.3 mm2)
    #                 [*** Based on simul. 12/12-18 use ap_dia ~ 9.0mm]
    # for localized_Z pattern: ap_dia ~ 4.81 mm (18.2 mm2 ~ 5.2x3.5 mm)