Unverified Commit eb795cc5 authored by acpaquette's avatar acpaquette Committed by GitHub
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Kaguyami App and Test Update (#4190) 

* Updated kaguyami app to new format

* Updated kaguyami2isis tests and added cropped test data

* Removed old makefile tests

* Updated kaguya cropping notebook to handle bands

* Updated kaguya proj test to fail
parent 74da682d

isis/notebooks/crop_kaguya.ipynb

+22 −80
Original line number Diff line number Diff line 
%% Cell type:code id: tags:



``` python

import pvl

import struct

import matplotlib.pyplot as plt

import numpy as np

import datetime

import os.path

import binascii

```



%% Cell type:code id: tags:



``` python

#kaguya_file = '/scratch/arsanders/kaguyatc/TC2S2B0_01_03043N107E3384.img'

#kaguya_file = '/home/arsanders/testData/apollo/AS15-M-1450.lbl'

kaguya_file = '/home/arsanders/testData/marci/MOI_000009_0294_MU_00N044W.IMG'

kaguya_file = '/Path/to/kaguyami/or/kaguyatc.img'

image_file = kaguya_file

```



%% Cell type:code id: tags:



``` python

header = pvl.load(kaguya_file)

```



%% Cell type:code id: tags:



``` python

header

```



%% Output



    PVLModule([

      ('PDS_VERSION_ID', 'PDS3')

      ('FILE_NAME', 'MOI_000009_0294_MU_00N044W.IMG')

      ('RECORD_TYPE', 'FIXED_LENGTH')

      ('RECORD_BYTES', 128)

      ('FILE_RECORDS', 2259)

      ('LABEL_RECORDS', 11)

      ('^IMAGE', 12)

      ('SPACECRAFT_NAME', 'MARS_RECONNAISSANCE_ORBITER')

      ('INSTRUMENT_NAME', 'MARS COLOR IMAGER')

      ('INSTRUMENT_HOST_NAME', 'MARS RECONNAISSANCE ORBITER')

      ('MISSION_PHASE_NAME', 'POSTMOI')

      ('TARGET_NAME', 'MARS')

      ('INSTRUMENT_ID', 'MARCI')

      ('PRODUCER_ID', 'MRO_MARCI_TEAM')

      ('DATA_SET_ID', 'MRO-M-MARCI-2-EDR-L0-V1.0')

      ('PRODUCT_CREATION_TIME',

       datetime.datetime(2007, 5, 17, 18, 31, 28, tzinfo=datetime.timezone.utc))

      ('SOFTWARE_NAME', 'makepds05 $Revision: 1.7 $')

      ('UPLOAD_ID', 'UNK')

      ('ORIGINAL_PRODUCT_ID', '4A_05_0001000200')

      ('PRODUCT_ID', 'MOI_000009_0294_MU_00N044W')

      ('START_TIME',

       datetime.datetime(2006, 3, 24, 4, 25, 53, 96000, tzinfo=datetime.timezone.utc))

      ('STOP_TIME',

       datetime.datetime(2006, 3, 24, 4, 55, 48, 296000, tzinfo=datetime.timezone.utc))

      ('SPACECRAFT_CLOCK_START_COUNT', '827641567:30')

      ('SPACECRAFT_CLOCK_STOP_COUNT', 'N/A')

      ('INTERFRAME_DELAY', Quantity(value=3.2, units='SECONDS'))

      ('FOCAL_PLANE_TEMPERATURE', Quantity(value=240.9, units='K'))

      ('SAMPLE_BIT_MODE_ID', 'SQROOT')

      ('LINE_EXPOSURE_DURATION', Quantity(value=3112.237, units='MSEC'))

      ('SAMPLING_FACTOR', 8)

      ('SAMPLE_FIRST_PIXEL', 0)

      ('FILTER_NAME', frozenset({'LONG_UV', 'SHORT_UV'}))

      ('RATIONALE_DESC', 'Post-MOI image of Argyre and Mare Erythraeum region')

      ('DATA_QUALITY_DESC', 'OK')

      ('ORBIT_NUMBER', 9)

      ('IMAGE',

       {'CHECKSUM': 12820826,

        'LINES': 2248,

        'LINE_PREFIX_BYTES': 0,

        'LINE_SAMPLES': 128,

        'LINE_SUFFIX_BYTES': 0,

        'SAMPLE_BITS': 8,

        'SAMPLE_BIT_MASK': 255,

        'SAMPLE_TYPE': 'UNSIGNED_INTEGER'})

    ])



%% Cell type:code id: tags:



``` python

header["^IMAGE"]

```



%% Output



    12



%% Cell type:code id: tags:



``` python

with open(kaguya_file, 'rb') as f:

    try:

        # For marci image

        image_offset = header['^IMAGE'] * header['LABEL_RECORDS'] * header["RECORD_BYTES"] - (header['IMAGE']['SAMPLE_BITS']//8)

        # image_offset = header['^IMAGE'] * header['LABEL_RECORDS'] * header["RECORD_BYTES"] - (header['IMAGE']['SAMPLE_BITS']//8)



        # For others

        # image_offset = header["^IMAGE"].value-(header['IMAGE']['SAMPLE_BITS']//8)

        image_offset = header["^IMAGE"].value-(header['IMAGE']['SAMPLE_BITS']//8)



        f.seek(image_offset)

        b_image_data = f.read()

    except AttributeError:

        # If detached label, "^IMAGE" will be a list.

        image_file = os.path.dirname(kaguya_file) + "/" + header["^IMAGE"][0]

        image_offset = header["^IMAGE"][1].value

        with open(image_file, 'rb') as im_f:

            b_image_data = im_f.read()

```



%% Cell type:code id: tags:



``` python

n_lines = 40

n_lines = 20

n_bands = 2

if "BANDS" not in header["IMAGE"].keys():

    n_bands = 1

line_length = header['IMAGE']['LINE_SAMPLES'] * (header['IMAGE']['SAMPLE_BITS']//8)

```



%% Cell type:code id: tags:



``` python

image_data = []

for j in range(n_lines):

    image_sample = np.frombuffer(b_image_data[j*line_length:(j+1)*line_length], dtype=np.int16, count=int(line_length/2))

    image_data.append(image_sample)

for i in range(n_bands):

    image_data.append([])

    for j in range(n_lines):

        image_sample = np.frombuffer(b_image_data[j*line_length:(j+1)*line_length], dtype=np.int16, count=int(line_length/2))

        image_data[i].append(image_sample)

image_data = np.array(image_data)

```



%% Cell type:code id: tags:



``` python

image_data.shape

image_data.min()

```



%% Output



    (40, 64)



%% Cell type:code id: tags:



``` python

plt.imshow(image_data)

plt.imshow(image_data[0])

```



%% Output



    <matplotlib.image.AxesImage at 0x10ec70fd0>





%% Cell type:code id: tags:



``` python

class RealIsisCubeLabelEncoder(pvl.encoder.ISISEncoder):

    def encode_time(self, value):

        if value.microsecond:

            second = u'%02d.%06d' % (value.second, value.microsecond)

        else:

            second = u'%02d' % value.second



        time = u'%02d:%02d:%s' % (value.hour, value.minute, second)

        return time

```



%% Cell type:code id: tags:



``` python

image_fn, image_ext = os.path.splitext(image_file)

crop = '_cropped'

mini_image_fn = image_fn + crop + image_ext

mini_image_bn = os.path.basename(mini_image_fn)



grammar = pvl.grammar.ISISGrammar()

grammar.comments+=(("#", "\n"), )

encoder = RealIsisCubeLabelEncoder()



# Overwrite the number of lines in the label

header['IMAGE']['LINES'] = n_lines

header['IMAGE']['BANDS'] = n_bands



if kaguya_file != image_file:

    # If detached label, point the mini label to the mini image

    header['^IMAGE'] = [mini_image_bn, pvlcollections.Units(1, 'BYTES')]

    header['FILE_NAME'] = mini_image_bn

else:

    # If attached label, calculate the new offset

    header['^IMAGE'] = pvl.collections.Units(len(pvl.dumps(header, encoder=encoder, grammar=grammar)), 'BYTES')

```



%% Cell type:code id: tags:



``` python

label_fn, label_ext = os.path.splitext(kaguya_file)

out_label = label_fn + crop + label_ext

print(out_label)



pvl.dump(header, out_label, encoder=encoder, grammar=grammar)

```



%% Output



    1820



%% Cell type:code id: tags:



``` python

with open(mini_image_fn, 'ab+') as f:

    b_reduced_image_data = image_data.tobytes()

    f.seek(0, 2)

    f.write(b_reduced_image_data)

```



%% Cell type:code id: tags:



``` python

pvl.load(mini_image_fn)

```



%% Cell type:code id: tags:



``` python

```

isis/src/kaguya/apps/kaguyami2isis/kaguyami2isis.cpp

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#include "kaguyami2isis.h"



#include <cstdio>

#include <string>

#include <sstream>

#include <iomanip>

#include <iostream>



#include "ProcessImportPds.h"

#include "ProgramLauncher.h"



#include "UserInterface.h"

#include "FileName.h"

#include "IString.h"



using namespace std;



static double range(double x);



namespace Isis {



  void kaguyami2isis(UserInterface &ui) {

    ProcessImportPds p;

    Pvl label;



    FileName inFile = ui.GetFileName("FROM");

    QString id;

    Pvl lab(inFile.expanded());



    if (lab.hasObject("IMAGE_MAP_PROJECTION")) {

      QString msg = "Unsupported projected file [" + inFile.expanded() + "]";

      throw IException(IException::User, msg, _FILEINFO_);

    }



    try {

      id = (QString) lab.findKeyword("DATA_SET_ID");

    }

    catch(IException &e) {

      QString msg = "Unable to read [DATA_SET_ID] from input file [" +

                    inFile.expanded() + "]";

      throw IException(e, IException::Unknown, msg, _FILEINFO_);

    }



    p.SetPdsFile(inFile.expanded(), "", label);

    CubeAttributeOutput &att = ui.GetOutputAttribute("TO");

    Cube *outcube = p.SetOutputCube(ui.GetFileName("TO"), att);



    // Get user entered special pixel ranges

    if(ui.GetBoolean("SETNULLRANGE")) {

      p.SetNull(ui.GetDouble("NULLMIN"), ui.GetDouble("NULLMAX"));

    }

    if(ui.GetBoolean("SETHRSRANGE")) {

      p.SetHRS(ui.GetDouble("HRSMIN"), ui.GetDouble("HRSMAX"));

    }

    if(ui.GetBoolean("SETHISRANGE")) {

      p.SetHIS(ui.GetDouble("HISMIN"), ui.GetDouble("HISMAX"));

    }

    if(ui.GetBoolean("SETLRSRANGE")) {

      p.SetLRS(ui.GetDouble("LRSMIN"), ui.GetDouble("LRSMAX"));

    }

    if(ui.GetBoolean("SETLISRANGE")) {

      p.SetLIS(ui.GetDouble("LISMIN"), ui.GetDouble("LISMAX"));

    }



    p.SetOrganization(Isis::ProcessImport::BSQ);



    p.StartProcess();



    // Get the directory where the Kaguya MI translation tables are.

    QString transDir = "$ISISROOT/appdata/translations/";

    Pvl inputLabel(inFile.expanded());

    Pvl *outputLabel = outcube->label();

    FileName transFile;



    // Translate the Archive group

    transFile = transDir + "KaguyaMiArchive.trn";

    PvlToPvlTranslationManager archiveXlater(inputLabel, transFile.expanded());

    archiveXlater.Auto(*(outputLabel));



    // Translate the Instrument group

    transFile = transDir + "KaguyaMiInstrument.trn";

    PvlToPvlTranslationManager instrumentXlater(inputLabel, transFile.expanded());

    instrumentXlater.Auto(*(outputLabel));

      //trim trailing z's from the time strings

    PvlGroup &instGroup(outputLabel->findGroup("Instrument",Pvl::Traverse));

    QString timeString;

      //StartTime

    PvlKeyword &startTimeKeyword=instGroup["StartTime"];

    timeString = startTimeKeyword[0];

    startTimeKeyword.setValue( timeString.mid(0,timeString.lastIndexOf("Z")) );

      //StartTimeRaw

    PvlKeyword &startTimeRawKeyword=instGroup["StartTimeRaw"];

    timeString = startTimeRawKeyword[0];

    startTimeRawKeyword.setValue( timeString.mid(0,timeString.lastIndexOf("Z")) );

      //StopTime

    PvlKeyword &stopTimeKeyword=instGroup["StopTime"];

    timeString = stopTimeKeyword[0];

    stopTimeKeyword.setValue( timeString.mid(0,timeString.lastIndexOf("Z")) );

      //StopTimeRaw

    PvlKeyword &stopTimeRawKeyword=instGroup["StopTimeRaw"];

    timeString = stopTimeRawKeyword[0];

    stopTimeRawKeyword.setValue( timeString.mid(0,timeString.lastIndexOf("Z")) );





    // Translate the BandBin group

    transFile = transDir + "KaguyaMiBandBin.trn";

    PvlToPvlTranslationManager bandBinXlater(inputLabel, transFile.expanded());

    bandBinXlater.Auto(*(outputLabel));



    //Set up the Kernels group

    PvlGroup kern("Kernels");

    QString baseBand = lab.findKeyword("BASE_BAND")[0];

    if (lab.findKeyword("INSTRUMENT_ID")[0] == "MI-VIS") {

      if (baseBand.contains("MV")) {

        kern += PvlKeyword("NaifFrameCode", toString(-13133) + baseBand[2]);

      }

      kern += PvlKeyword("NaifCkCode", toString(-131330));

    }

    else if (lab.findKeyword("INSTRUMENT_ID")[0] == "MI-NIR") {

      if (baseBand.contains("MN")) {

        kern += PvlKeyword("NaifFrameCode", toString(-13134) + baseBand[2]);

      }

      kern += PvlKeyword("NaifCkCode", toString(-131340));

    }



    //At the time of this writing there was no expectation that Kaguya ever did any binning

    //  so this is check to make sure an error is thrown if an image was binned

    if (lab.findKeyword("INSTRUMENT_ID")[0] == "MI-VIS" && outcube->sampleCount() != 962 ) {

      QString msg = "Input file [" + inFile.expanded() + "]" + " appears to be binned.  Binning was "

                    "unexpected, and is unsupported by the camera model";

      throw IException(IException::Unknown, msg, _FILEINFO_);

    }

    if (lab.findKeyword("INSTRUMENT_ID")[0] == "MI-NIR" && outcube->sampleCount() != 320 ) {

      QString msg = "Input file [" + inFile.expanded() + "]" + " appears to be binned.  Binning was "

                    "unexpected, and is unsupported by the camera model";

      throw IException(IException::Unknown, msg, _FILEINFO_);

    }



    outcube->putGroup(kern);



    p.EndProcess();

  }



  double range(double x) {

    double a,b,c;

    b = x / 360;

    if(b > 0) {

      c = floor(b);

    }

    else {

      c = ceil(b);

    }

    a = 360 * (b - c);

    if(a < 0) {

      a = a + 360;

    }

    return a;

  }

}

isis/src/kaguya/apps/kaguyami2isis/kaguyami2isis.h

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#ifndef kaguyami2isis_h

#define kaguyami2isis_h



#include "UserInterface.h"



namespace Isis {

  extern void kaguyami2isis(UserInterface &ui);

}



#endif

isis/src/kaguya/apps/kaguyami2isis/main.cpp

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isis/src/kaguya/apps/kaguyami2isis/tsts/Makefile

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BLANKS = "%-6s"    

LENGTH = "%-40s"



include $(ISISROOT)/make/isismake.tststree