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Fix error in initial commit template, add documentation for encoding
1 parent 769c7eb commit 8403d7f

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lines changed

‎LICENSE.txt

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -65,4 +65,4 @@ In no event and under no legal theory, whether in tort (including negligence), c
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While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability.
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END OF TERMS AND CONDITIONS
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END OF TERMS AND CONDITIONS

‎MSNumpressFSharp.sln

Lines changed: 13 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = ".paket", ".paket", "{63297B
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}"
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EndProject
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Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "MSNumpressFSharp", "src\MSNumpressFSharp\MSNumpressFSharp.fsproj", "{082A81A9-8F10-41E0-A567-97A23493E208}"
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Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "MSNumpressFSharp", "src\MSNumpressFSharp\MSNumpressFSharp.fsproj", "{72EA463B-C958-474C-BDDC-F5541985E33D}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "project", "project", "{BF60BC93-E09B-4E5F-9D85-95A519479D54}"
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ProjectSection(SolutionItems) = preProject
@@ -28,13 +28,15 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tools", "tools", "{83F16175
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "content", "content", "{8E6D5255-776D-4B61-85F9-73C37AA1FB9A}"
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ProjectSection(SolutionItems) = preProject
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docsrc\content\Decoding.fsx = docsrc\content\Decoding.fsx
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docsrc\content\Encoding.fsx = docsrc\content\Encoding.fsx
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docsrc\content\index.fsx = docsrc\content\index.fsx
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docsrc\content\tutorial.fsx = docsrc\content\tutorial.fsx
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EndProjectSection
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{ED8079DD-2B06-4030-9F0F-DC548F98E1C4}"
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EndProject
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Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "MSNumpressFSharp.Tests", "tests\MSNumpressFSharp.Tests\MSNumpressFSharp.Tests.fsproj", "{157660D1-5DA5-4A89-9708-CEE6CFF623A7}"
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Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "MSNumpressFSharp.Tests", "tests\MSNumpressFSharp.Tests\MSNumpressFSharp.Tests.fsproj", "{C819829A-8C8F-48DC-9C93-7DD11F08EE43}"
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EndProject
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "git", "git", "{078A9C52-DDC1-46F4-9235-9E6C89C87AFD}"
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ProjectSection(SolutionItems) = preProject
@@ -45,7 +47,6 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "git", "git", "{078A9C52-DDC
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.github\CONTRIBUTING.md = .github\CONTRIBUTING.md
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.github\ISSUE_TEMPLATE\feature_request.md = .github\ISSUE_TEMPLATE\feature_request.md
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.github\ISSUE_TEMPLATE.md = .github\ISSUE_TEMPLATE.md
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LICENSE.txt = LICENSE.txt
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PULL_REQUEST_TEMPLATE.md = PULL_REQUEST_TEMPLATE.md
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EndProjectSection
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EndProject
@@ -67,14 +68,14 @@ Global
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Release|Any CPU = Release|Any CPU
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EndGlobalSection
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GlobalSection(ProjectConfigurationPlatforms) = postSolution
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{082A81A9-8F10-41E0-A567-97A23493E208}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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{082A81A9-8F10-41E0-A567-97A23493E208}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{082A81A9-8F10-41E0-A567-97A23493E208}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{082A81A9-8F10-41E0-A567-97A23493E208}.Release|Any CPU.Build.0 = Release|Any CPU
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{157660D1-5DA5-4A89-9708-CEE6CFF623A7}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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{157660D1-5DA5-4A89-9708-CEE6CFF623A7}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{157660D1-5DA5-4A89-9708-CEE6CFF623A7}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{157660D1-5DA5-4A89-9708-CEE6CFF623A7}.Release|Any CPU.Build.0 = Release|Any CPU
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{72EA463B-C958-474C-BDDC-F5541985E33D}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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{72EA463B-C958-474C-BDDC-F5541985E33D}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{72EA463B-C958-474C-BDDC-F5541985E33D}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{72EA463B-C958-474C-BDDC-F5541985E33D}.Release|Any CPU.Build.0 = Release|Any CPU
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{C819829A-8C8F-48DC-9C93-7DD11F08EE43}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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{C819829A-8C8F-48DC-9C93-7DD11F08EE43}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{C819829A-8C8F-48DC-9C93-7DD11F08EE43}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{C819829A-8C8F-48DC-9C93-7DD11F08EE43}.Release|Any CPU.Build.0 = Release|Any CPU
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{B7339FEC-0891-4DF8-8BB5-0B806A64F32F}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
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{B7339FEC-0891-4DF8-8BB5-0B806A64F32F}.Debug|Any CPU.Build.0 = Debug|Any CPU
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{B7339FEC-0891-4DF8-8BB5-0B806A64F32F}.Release|Any CPU.ActiveCfg = Release|Any CPU
@@ -86,7 +87,7 @@ Global
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GlobalSection(NestedProjects) = preSolution
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{83F16175-43B1-4C90-A1EE-8E351C33435D} = {A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}
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{8E6D5255-776D-4B61-85F9-73C37AA1FB9A} = {A6A6AF7D-D6E3-442D-9B1E-58CC91879BE1}
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{157660D1-5DA5-4A89-9708-CEE6CFF623A7} = {ED8079DD-2B06-4030-9F0F-DC548F98E1C4}
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{C819829A-8C8F-48DC-9C93-7DD11F08EE43} = {ED8079DD-2B06-4030-9F0F-DC548F98E1C4}
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EndGlobalSection
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GlobalSection(ExtensibilityGlobals) = postSolution
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SolutionGuid = {D55EAFC0-7966-48AB-9DF6-8CFA23ABABB1}

‎README.md

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@@ -2,4 +2,4 @@
22

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This is a F# port of the C# version of the MS Numpress library. The original library can be found at https://github.com/ms-numpress/ms-numpress.
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The library provides three algorithms for compression of mass spectrometry data. One algorithm is designed for the compression of linear data like retention time or m/z data. The other two algorithms are for compression of non-linear data with lower precision requirements, such as ion count data.
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The library provides three algorithms for compression of mass spectrometry data. One algorithm is designed for the compression of linear data like retention time or m/z data. The other two algorithms are for compression of non-linear data with lower precision requirements, such as ion count data.

‎build.fsx

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Original file line numberDiff line numberDiff line change
@@ -282,11 +282,11 @@ let githubLink = sprintf "https://github.com/%s/%s" github_release_user gitName
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// Specify more information about your project
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let info =
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[ "project-name", "FSharpGephiStreamer"
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"project-author", "Timo M�hlhaus"
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"project-summary", "FSharp functions for streaming graph data to gephi a graph visualization tool"
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[ "project-name", "MSNumpressFSharp"
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"project-author", "Jonathan Ott"
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"project-summary", "F# port of the MSNumpress library."
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"project-github", githubLink
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"project-nuget", "http://nuget.org/packages/FSharpGephiStreamer" ]
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"project-nuget", "http://nuget.org/packages/MSNumpressFSharp" ]
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let root = website
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‎docsrc/content/Decoding.fsx

Whitespace-only changes.

‎docsrc/content/Encoding.fsx

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@@ -0,0 +1,95 @@
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(*** hide ***)
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#I "../../bin"
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#r @"MSNumpressFSharp\net47\MSNumpressFSharp.dll"
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open MSNumpressFSharp
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(**
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###Numpress Pic
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This compression algorithm is intended for ion count data.
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It rounds values to the nearest integer, and stores these integers in a truncated
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form which is effective for values relatively close to zero.
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The encodePic function takes an array with data, the length of this array and a byte array
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where the encoded bytes are stored. The maximum size of the byte array is n * 5,
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but usually it is smaller depending on the data. The function modifies the byte array and returns
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the number of encoded bytes.
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*)
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//sample data
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let dataPic = [|1. .. 100.|]
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//empty array for the encoded bytes
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let byteArrayPic: byte[] = Array.zeroCreate (dataPic.Length * 5)
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//takes data, data length and an empty array for the encoded bytes. Returns the number of encoded bytes.
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let encodePic = MSNumpressFSharp.Encode.encodePic (dataPic, dataPic.Length, byteArrayPic)
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29+
(**
30+
byteArrayPic contains now the compressed data. The byte array and number of encoded bytes is needed for
31+
decoding.
32+
33+
###Numpress Lin
34+
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This compression uses a fixed point representation, achieved by multiplication with a scaling factor
36+
and rounding to the nearest integer. To exploit the assumed linearity of the data, linear prediction is
37+
then used.The scaling factor can be chosen manually, but the library also contains a function for
38+
retrieving the optimal linear scaling factor for a given data array. Since the scaling factor is variable,
39+
it is stored as a regular double precision float first in the encoding, and automatically parsed during
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decoding.
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The encodeLinear function takes an array with data, the length of this array, a byte array where the encoded bytes
43+
are stored and a linear scaling factor.The maximum size of the byte array is 8 + n * 5,
44+
but usually it is smaller depending on the data. The function modifies the byte array and returns
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the number of encoded bytes.
46+
*)
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//sample data
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let dataLin = [|1. .. 100.|]
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//empty array for the encoded bytes
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let byteArrayLin: byte[] = Array.zeroCreate (8 + dataLin.Length * 5)
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//optimal scaling factor for sample data
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let optimalFixedPointLin = MSNumpressFSharp.Encode.optimalLinearFixedPoint (dataLin, dataLin.Length)
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//takes data, data length, an empty array for the encoded bytes and a scaling factor. Returns the number of encoded bytes.
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let encodeLin = MSNumpressFSharp.Encode.encodeLinear (dataLin, dataLin.Length, byteArrayLin, optimalFixedPointLin)
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(**
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byteArrayLin contains now the compressed data. The byte array and number of encoded bytes is needed for
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decoding.
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###Numpress Slof
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This function also targets ion count data. The compression takes the natural logarithm of values, multiplies it
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by a scaling factor and rounds to the nearest integer. For typical ion count dynamic ranges these
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values fits into two byte integers, so only the two least significant bytes of the integer are stored.
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The scaling factor can be chosen manually, but the library also contains a function for retrieving
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the optimal Slof scaling factor for a given data array. Since the scaling factor is variable, it is
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stored as a regular double precision float first in the encoding, and automatically parsed during
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decoding.
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The encodeSlof function takes an array with data, the length of this array, a byte array where the encoded bytes
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are stored and a linear scaling factor.The maximum size of the byte array is n * 2 + 8,
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but usually it is smaller depending on the data. The function modifies the byte array and returns
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the number of encoded bytes.
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*)
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//sample data
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let dataSlof = [|1. .. 100.|]
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//empty array for the encoded bytes
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let byteArraySlof: byte[] = Array.zeroCreate (8 + dataSlof.Length * 2)
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//optimal scaling factor for sample data
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let optimalFixedPointSlof = MSNumpressFSharp.Encode.optimalSlofFixedPoint (dataSlof, dataSlof.Length)
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//takes data, data length, an empty array for the encoded bytes and a scaling factor. Returns the number of encoded bytes.
90+
let encodeSlof = MSNumpressFSharp.Encode.encodeSlof (dataSlof, dataSlof.Length, byteArraySlof, optimalFixedPointSlof)
91+
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(**
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byteArrayLin contains now the compressed data. The byte array and number of encoded bytes is needed for
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decoding.
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*)

‎docsrc/tools/templates/template.cshtml

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<div class="span3">
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<img src="@Root/img/logo.png" alt="F# Project" style="width:150px;margin:10px" />
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<ul class="nav nav-list" id="menu" style="margin-top: 20px;">
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<li class="nav-header">@Properties["project-name"]</li>
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<li><a href="@Root/index.html">Home page</a></li>
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<li class="divider"></li>
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<li><a href="@Properties["project-nuget"]">Get Library via NuGet</a></li>
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<li><a href="@Properties["project-github"]">Source Code on GitHub</a></li>
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<li><a href="@Root/license.html">License</a></li>
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<li><a href="@Root/release-notes.html">Release Notes</a></li>
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<li class="nav-header">Getting started</li>
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<li><a href="@Root/tutorial.html">Sample tutorial</a></li>
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<li class="nav-header">@Properties["project-name"]</li>
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<li><a href="@Root/index.html">Home page</a></li>
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<li class="divider"></li>
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<li><a href="@Properties["project-nuget"]">Get Library via NuGet</a></li>
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<li><a href="@Properties["project-github"]">Source Code on GitHub</a></li>
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<li><a href="@Root/license.html">License</a></li>
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<li><a href="@Root/release-notes.html">Release Notes</a></li>
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<li class="nav-header">Documentation</li>
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<li><a href="@Root/reference/index.html">API Reference</a></li>
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<li class="nav-header">Getting started</li>
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<li><a href="@Root/tutorial.html">Sample tutorial</a></li>
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<li class="nav-header">Documentation</li>
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<li><a href="@Root/reference/index.html">API Reference</a></li>
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<li class="nav-header">Encoding</li>
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<li><a href="@Root/reference/index.html">API Reference</a></li>
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<li class="nav-header">Decoding</li>
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<li><a href="@Root/reference/index.html">API Reference</a></li>
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</ul>
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</div>
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</div>

‎src/MSNumpressFSharp/AssemblyInfo.fs

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1+
// Auto-Generated by FAKE; do not edit
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namespace System
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open System.Reflection
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[<assembly: AssemblyTitleAttribute("MSNumpressFSharp")>]
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[<assembly: AssemblyProductAttribute("MSNumpressFSharp")>]
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[<assembly: AssemblyDescriptionAttribute("A short summary of your project.")>]
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[<assembly: AssemblyVersionAttribute("1.0")>]
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[<assembly: AssemblyFileVersionAttribute("1.0")>]
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[<assembly: AssemblyDescriptionAttribute("F# port of the MSNumpress library.")>]
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[<assembly: AssemblyVersionAttribute("0.0.1")>]
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[<assembly: AssemblyFileVersionAttribute("0.0.1")>]
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[<assembly: AssemblyConfigurationAttribute("Release")>]
911
do ()
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1113
module internal AssemblyVersionInformation =
12-
let [<Literal>] Version = "1.0"
14+
let [<Literal>] AssemblyTitle = "MSNumpressFSharp"
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let [<Literal>] AssemblyProduct = "MSNumpressFSharp"
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let [<Literal>] AssemblyDescription = "F# port of the MSNumpress library."
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let [<Literal>] AssemblyVersion = "0.0.1"
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let [<Literal>] AssemblyFileVersion = "0.0.1"
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let [<Literal>] AssemblyConfiguration = "Release"

‎src/MSNumpressFSharp/MSNumpress.fs

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Original file line numberDiff line numberDiff line change
@@ -431,4 +431,4 @@ module Decode =
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loop (i + 2) (riV + 1)
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| value when value >= dataSize -> riV
433433
| _ -> failwith "Error in decodeSlof. dataSize may be wrong."
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loop 8 0
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loop 8 0

‎src/MSNumpressFSharp/MSNumpressFSharp.fsproj

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@@ -1,4 +1,4 @@
1-
<Project Sdk="Microsoft.NET.Sdk">
1+
<Project Sdk="Microsoft.NET.Sdk">
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<PropertyGroup>
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<TargetFrameworks>net45;net47;netstandard2.0</TargetFrameworks>
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<RootNamespace>MSNumpressFSharp</RootNamespace>

‎src/MSNumpressFSharpConsole/AssemblyInfo.fs

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
// Auto-Generated by FAKE; do not edit
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namespace System
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open System.Reflection
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[<assembly: AssemblyTitleAttribute("MSNumpressFSharpConsole")>]
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[<assembly: AssemblyProductAttribute("MSNumpressFSharp")>]
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[<assembly: AssemblyDescriptionAttribute("F# port of the MSNumpress library.")>]
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[<assembly: AssemblyVersionAttribute("0.0.1")>]
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[<assembly: AssemblyFileVersionAttribute("0.0.1")>]
10+
[<assembly: AssemblyConfigurationAttribute("Release")>]
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do ()
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module internal AssemblyVersionInformation =
14+
let [<Literal>] AssemblyTitle = "MSNumpressFSharpConsole"
15+
let [<Literal>] AssemblyProduct = "MSNumpressFSharp"
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let [<Literal>] AssemblyDescription = "F# port of the MSNumpress library."
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let [<Literal>] AssemblyVersion = "0.0.1"
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let [<Literal>] AssemblyFileVersion = "0.0.1"
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let [<Literal>] AssemblyConfiguration = "Release"

‎temp/gh-pages/Decoding.html

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8"/>
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<title>Decoding</title>
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<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
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<meta name="description" content="F# port of the MSNumpress library."/>
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<meta name="author" content="Jonathan Ott"/>
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<script src="https://code.jquery.com/jquery-1.8.0.js"></script>
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<script src="https://code.jquery.com/ui/1.8.23/jquery-ui.js"></script>
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<script src="https://netdna.bootstrapcdn.com/twitter-bootstrap/2.2.1/js/bootstrap.min.js"></script>
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<link href="https://netdna.bootstrapcdn.com/twitter-bootstrap/2.2.1/css/bootstrap-combined.min.css" rel="stylesheet"/>
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<meta http-equiv="X-UA-Compatible" content="IE=11" >
15+
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
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<link type="text/css" rel="stylesheet" href="content/style.css" /> <!--/MSNumpressFSharp-->
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<link type="text/css" rel="stylesheet" href="style/CSBstyles.css" /> <!--/MSNumpressFSharp-->
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<script type="text/javascript" src="content/tips.js"></script> <!--/MSNumpressFSharp-->
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<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
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<!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
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<![endif]-->
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</head>
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<body>
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<div class="container">
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<div class="masthead">
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<ul class="nav nav-pills pull-right">
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<li><a href="http://fsharp.org">fsharp.org</a></li>
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<li><a href="https://github.com/Joott/MSNumpressFSharp">github page</a></li>
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</ul>
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<h3 class="muted"><a href="index.html">MSNumpressFSharp</a></h3>
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</div>
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<hr />
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<div class="row">
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<div class="span9" id="main">
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</div>
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<div class="span3">
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<img src="img/logo.png" alt="F# Project" style="width:150px;margin:10px" />
42+
<ul class="nav nav-list" id="menu" style="margin-top: 20px;">
43+
<li class="nav-header">MSNumpressFSharp</li>
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<li><a href="index.html">Home page</a></li>
45+
<li class="divider"></li>
46+
<li><a href="http://nuget.org/packages/MSNumpressFSharp">Get Library via NuGet</a></li>
47+
<li><a href="https://github.com/Joott/MSNumpressFSharp">Source Code on GitHub</a></li>
48+
<li><a href="license.html">License</a></li>
49+
<li><a href="release-notes.html">Release Notes</a></li>
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51+
<li class="nav-header">Getting started</li>
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<li><a href="tutorial.html">Sample tutorial</a></li>
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<li class="nav-header">Documentation</li>
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<li><a href="reference/index.html">API Reference</a></li>
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<li class="nav-header">Encoding</li>
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<li><a href="reference/index.html">API Reference</a></li>
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<li class="nav-header">Decoding</li>
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<li><a href="reference/index.html">API Reference</a></li>
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</ul>
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</div>
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</div>
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