Re: [netcdfgroup] Chemstation can't read my files

• To: "Kassan, Scott - OI Analytical" <Scott.Kassan@xxxxxxx>
• Subject: Re: [netcdfgroup] Chemstation can't read my files
• From: Mark Tracy <tracy454@xxxxxxxxx>
• Date: Wed, 13 Apr 2011 22:58:05 -0700

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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