dvinfo

#!/usr/bin/env python
"""
dvinfo: text dump of metadata from a DeltaVision file
author: graemeball@googlemail.com, 2013
license: GPL
"""

import sys
import numpy as np
import collections


# check we were passed 1 filename
if len(sys.argv) != 2:
    print("\n  Usage: dvinfo <filename1>")
    print("\n    dumps metadata stored in a DeltaVision file header")
    sys.exit(0)


### Data type & helper function definitions

# Imsubs file header, see http://msg.ucsf.edu/IVE/IVE4_HTML/IM_ref2.html
DV_HDR_STRUCT = [
    ('3i4', 'Num'),
    ('1i4', 'PixelType'),
    ('3i4', 'mst'),
    ('3i4', 'm'),
    ('3f4', 'd'),
    ('3f4', 'angle'),
    ('3i4', 'axis'),
    ('3f4', 'mmm1'),
    ('1i4', 'nspg'),
    ('1i4', 'next'),
    ('1i2', 'dvid'),
    ('1i2', 'nblank'),
    ('1i4', 'ntst'),
    ('24a1', 'blank'),
    ('1i2', 'NumIntegers'),
    ('1i2', 'NumFloats'),
    ('1i2', 'sub'),
    ('1i2', 'zfac'),
    ('2f4', 'mm2'),
    ('2f4', 'mm3'),
    ('2f4', 'mm4'),
    ('1i2', 'type'),
    ('1i2', 'LensNum'),
    ('1i2', 'n1'),
    ('1i2', 'n2'),
    ('1i2', 'v1'),
    ('1i2', 'v2'),
    ('2f4', 'mm5'),
    ('1i2', 'NumTimes'),
    ('1i2', 'ImgSequence'),
    ('3f4', 'tilt'),
    ('1i2', 'NumWaves'),
    ('5i2', 'wave'),
    ('3f4', 'zxy0'),
    ('1i4', 'NumTitles'),
    ('10a80', 'Titles')
]

# API / DeltaVision non-standard metadata
API_TYPE = 100
# TODO, add channels 4 and 5 to lookup: presumably follows Ch3 in Title6
LOOKUP_API_META = collections.OrderedDict([
    ['Ch1_Min', ('f4', 5, 76, 80, 0.0)],
    ['Ch1_Max', ('f4', 6, 0, 4, 0.0)],
    ['Ch1_Exp', ('f4', 6, 4, 8, 1.0)],
    ['Ch2_Min', ('f4', 6, 8, 12, 0.0)],
    ['Ch2_Max', ('f4', 6, 12, 16, 0.0)],
    ['Ch2_Exp', ('f4', 6, 16, 20, 1.0)],
    ['Ch3_Min', ('f4', 6, 20, 24, 0.0)],
    ['Ch3_Max', ('f4', 6, 24, 28, 0.0)],
    ['Ch3_Exp', ('f4', 6, 28, 32, 1.0)]
    ])  # 'key', (format, nTitle, char_1st, char_last + 1, default)


def chars_to_float(chars):
    """
    Convert a string of 4 chars to a single precision float
    """
    #return [hex(ord(x)) for x in chars]  # hex chars for debugging
    if chars == '\x00\x00\x00\x00':
        # TODO: should be 0 for float32 -- why does softWoRx show 1.0?
        return 1.00
    else:
        return np.fromstring(chars, dtype=np.float32)[0]

# lookup table for conversion functions
CHARS_TO_PY = {
    'f4': chars_to_float
}

# END data type & helper function definitions


def main():
    """
    Read DeltaVision file header into numpy recarray and dump text info
    """
    imsubs_file = open(sys.argv[1], 'rb')
    formats = [fmt_lbl[0] for fmt_lbl in DV_HDR_STRUCT]
    labels = [fmt_lbl[1] for fmt_lbl in DV_HDR_STRUCT]
    hdr_arr = np.rec.fromfile(imsubs_file, formats=formats, shape=1)
    hdr = collections.OrderedDict(zip(labels, hdr_arr[0]))
    print("\nImsubs file standard metadata:-")
    print_hdr(hdr)
    imsubs_file.close()


def print_hdr(hdr):
    """
    Print Imsubs / DeltaVision header fields (dict) in header byte order,
    including API metadata stored in Title fields if appropriate.
    """
    for entry in hdr:
        print("  {0}: {1}".format(entry, hdr[entry]))
    if 'type' in hdr and hdr['type'] == API_TYPE:
        print("\nAPI / Deltavision non-standard metadata:-")
        # recursive call, since this function prints key, value pairs
        print_hdr(extract_api_meta(hdr['Titles']))


def extract_api_meta(titles):
    """
    Extract a dictionary of API metadata entries from title fields
    """
    meta = collections.OrderedDict()
    for key in LOOKUP_API_META:
        try:
            to_py_type = CHARS_TO_PY[LOOKUP_API_META[key][0]]
            ixs = LOOKUP_API_META[key][1:]
            meta[key] = to_py_type(titles[ixs[0]][ixs[1]:ixs[2]])
        except IndexError:
            meta[key] = LOOKUP_API_META[key][4]
    return meta


if __name__ == '__main__':
    main()