Scott,
The AIA mass-spectrometry format permits short (16-bit), long (32-bit), float
(32-bit) or double (64-bit) for the mass, the time and the intensity. Default
for intensity is "long" otherwise you need to set the
intensity-axis-data-format to "double." Similarly, the default for time and
mass is "short."
My software is read-only so I just coerced everything to double when read. You
are going the other way. I guess that Chemstation cares about data format. You
might end up writing the data as "long" and using the
intensity-axis-scale-factor which is a double. On the other hand, maybe
Chemstation will honor the intensity-axis-data-format setting. Have you tried
feeding the sample data at andi.sourceforge.net to Chemstation?
If you want, you can send me one of your sample data files and I will see what
my software makes of it.
Mark Tracy
www.mt-se.com
On Apr 13, 2011, at 10:36 AM, Kassan, Scott - OI Analytical wrote:
> I'm having trouble generating files that Chemstation, and I assume
> other data consumers, has trouble with. The trouble lies in the array
> of intensity_values. I'm writing doubles to that array. The array is
> identified as containing doubles in the variables definition section.
> However, when Chemstation reads the values, it appears to be
> interpreting them as longs. But AMDIS seems to be able to read
> the values correctly.
>
> I've tried adding the global attribute raw_data_intensity_format = "Double",
> but that did not help.
>
> Below is an excerpt of an ncdump of one of my data files. Any help steering
> me in the right direction would be greatly appreciated.
>
> netcdf 100ppm_010 {
> dimensions:
> point_number = UNLIMITED ; // (5182 currently)
> scan_number = 845 ;
> variables:
> double scan_acquisition_time(scan_number) ;
> int actual_scan_number(scan_number) ;
> double total_intensity(scan_number) ;
> total_intensity:units = "Arbitrary Intensity Units" ;
> double mass_range_min(scan_number) ;
> double mass_range_max(scan_number) ;
> int scan_index(scan_number) ;
> int point_count(scan_number) ;
> int flag_count(scan_number) ;
> short mass_values(point_number) ;
> mass_values:units = "M/Z" ;
> mass_values:scale_factor = 1. ;
> double intensity_values(point_number) ;
> intensity_values:units = "Arbitrary Intensity Units" ;
> intensity_values:scale_factor = 1. ;
>
> // global attributes:
> :ms_template_revision = "1.0.1" ;
> :dataset_completeness = "C1+C2" ;
> :netcdf_revision = "3.6.1 of Mar 7 2006 14:13:30 $" ;
> :experiment_date_time_stamp = "20100911172102+0000" ;
> :netcdf_file_date_time_stamp = "20100911172102+0000" ;
> :experiment_type = "Centroided Mass Spectrum" ;
> :languages = "English" ;
> :test_comments = "100 ppm" ;
> :actual_runtime_length = 89.974755 ;
> :global_mass_min = 7 ;
> :global_mass_max = 199 ;
> ...
>
> data:
>
> scan_acquisition_time = 0, 0.106479, 0.212958, 0.319437, 0.425916, 0.532395,
> 0.638874, 0.745353, 0.851832, 0.958311, 1.06479, 1.171269, 1.277748,
> 1.384227, 1.490706, 1.597185, 1.703664, 1.810143, 1.916622, 2.023101,
> 2.12958, 2.236059, 2.342538, 2.449017, 2.555496, 2.661975, 2.768454,
> ...
>
> actual_scan_number = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
> 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
> 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
> 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,
> ...
>
> total_intensity = 10.8773901760578, 18.6721186637878, 17.6812633574009,
> 17.0867496728897, 8.80760312080383, 16.2280081063509, 14.8187923133373,
> 9.09385061264038, 11.2296939492226, 13.2114050388336, 11.2737315893173,
> 12.9912151098251, 12.7490055561066, 15.1710965037346, 14.180241510272,
> ...
>
> mass_range_min = 45, 43, 43, 43, 42, 42, 42, 43, 43, 43, 42, 43, 43, 42, 43,
> 43, 45, 43, 45, 43, 43, 43, 43, 43, 43, 43, 43, 42, 42, 42, 42, 43, 43,
> 43, 45, 43, 43, 45, 43, 43, 45, 43, 43, 43, 43, 43, 43, 43, 43, 42, 43,
> 42, 43, 43, 43, 43, 42, 55, 43, 42, 45, 43, 45, 45, 45, 43, 42, 43, 43,
> ...
>
> mass_range_max = 70, 166, 147, 154, 46, 97, 66, 45, 105, 76, 45, 131, 119,
> 143, 154, 127, 55, 117, 69, 69, 163, 92, 141, 146, 133, 127, 76, 57, 150,
> 66, 146, 146, 91, 132, 118, 56, 141, 118, 81, 141, 132, 141, 77, 132,
> 132, 70, 56, 125, 121, 57, 105, 145, 57, 68, 136, 133, 101, 93, 55, 57,
> ...
>
> scan_index = 0, 5, 14, 22, 30, 33, 40, 46, 48, 53, 58, 61, 65, 70, 76, 83,
> 88, 90, 95, 99, 102, 111, 117, 123, 127, 135, 141, 145, 150, 158, 164,
> 173, 178, 183, 186, 190, 194, 202, 207, 215, 220, 227, 236, 242, 249,
> 256, 262, 267, 274, 279, 284, 293, 302, 307, 312, 320, 329, 334, 337,
> ...
>
> point_count = 5, 9, 8, 8, 3, 7, 6, 2, 5, 5, 3, 4, 5, 6, 7, 5, 2, 5, 4, 3, 9,
> 6, 6, 4, 8, 6, 4, 5, 8, 6, 9, 5, 5, 3, 4, 4, 8, 5, 8, 5, 7, 9, 6, 7, 7,
> 6, 5, 7, 5, 5, 9, 9, 5, 5, 8, 9, 5, 3, 3, 4, 7, 5, 6, 4, 4, 5, 13, 4, 3,
> 6, 6, 7, 5, 4, 4, 2, 8, 7, 7, 8, 5, 5, 8, 4, 5, 5, 2, 3, 6, 5, 5, 6, 11,
> ...
>
> flag_count = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> ...
>
> mass_values = 45, 55, 57, 60, 70, 43, 45, 46, 55, 57, 70, 110, 154, 166, 43,
> 45, 46, 55, 57, 70, 110, 147, 43, 45, 55, 57, 69, 83, 150, 154, 42, 45,
> 46, 42, 43, 45, 57, 66, 73, 97, 42, 43, 45, 52, 55, 66, 43, 45, 43, 45,
> 57, 80, 105, 43, 45, 46, 61, 76, 42, 43, 45, 43, 45, 67, 131, 43, 45, 79,
> ...
>
> intensity_values = 5.5487904548645, 2.46612882614136, 1.56334948539734,
> 0.462399154901505, 0.836722254753113, 4.60197257995605, 6.07724618911743,
> 1.32114052772522, 2.31199598312378, 1.07893133163452, 0.814703285694122,
> 0.616532206535339, 1.65142548084259, 0.198171079158783, 5.24052381515503,
> ...
>
>
> *****************************************************************
> Scott Kassan
> Senior Software Engineer
> ITT | OI Analytical
> 2148 Pelham Parkway
> Building 400
> Pelham, AL 35124
>
> T: (205) 733-6900 x259
> F: (205) 733-6919
> Email: scott.kassan@xxxxxxx
> *****************************************************************
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