Cleaning out absolute paths (#461)

%% Cell type:markdown id: tags:

# Writing out a USGSCSM ISD from a PDS3 Dawn Framing Camera image

%% Cell type:code id: tags:

``` python

import os

import json

import ale

from ale.drivers.dawn_drivers import DawnFcPds3NaifSpiceDriver

from ale.formatters.usgscsm_formatter import to_usgscsm

```

%% Cell type:markdown id: tags:

## Instantiating an ALE driver

ALE drivers are objects that define how to acquire common ISD keys from an input image format, in this case we are reading in a PDS3 image using NAIF SPICE kernels for exterior orientation data. If the driver utilizes NAIF SPICE kernels, it is implemented as a [context manager](https://docs.python.org/3/reference/datamodel.html#context-managers) and will furnish metakernels when entering the context (i.e. when entering the `with` block) and free the metakernels on exit. This maintains the integrity of spicelib's internal data structures. These driver objects are short-lived and are input to a formatter function that consumes the API to create a serializable file format. `ale.formatters` contains available formatter functions.

The default config file is located at `ale/config.yml` and is copied into your home directory at `.ale/config.yml` on first use of the library. The config file can be modified using a text editor. `ale.config` is loaded into memory as a dictionary. It is used to find metakernels for different missions. For example, there is an entry for Dawn that points to `/usgs/cpkgs/isis3/data/dawn/kernels/mk/` by default. If you want to use your own metakernels, you will need to udpate this path. For example, if the metakernels are located in `/data/dawn/mk/` the Dawn entry should be updated with this path. If you are using the default metakernels, then you do not need to update the path.

ALE has a two step process for writing out an ISD: 1. Instantiate your driver (in this case `DawnFcPds3LabelNaifSpiceDriver`) within a context and 2. pass the driver object into a formatter (in this case, `to_usgscsm`).

Requirements:

 * A PDS3 Dawn image

 * NAIF metakernels installed

 * Config file path for Dawn (ale.config.dawn) pointing to Dawn NAIF metakernel directory

 * A conda environment with ALE installed into it usisng the `conda install` command or created using the environment.yml file at the base of ALE.

%% Cell type:code id: tags:

``` python

# printing config displays the yaml formatted string

print(ale.config)

# config object is a dictionary so it has the same access patterns

print('Dawn spice directory:', ale.config['dawn'])

# updating config for new Dawn path in this notebook

# Note: this will not change the path in `.ale/config.yml`. This change only lives in the notebook.

# ale.config['dawn'] = '/scratch/jlaura/spice/dawn-m_a-spice-6-v1.0/dawnsp_1000/extras/mk/'

```

%% Output

    cassini: /usgs/cpkgs/isis3/data/cassini/kernels/mk/

    dawn: /data/spice/dawn-m_a-spice-6-v1.0/dawnsp_1000/extras/mk

    kaguya: /data/spice/SELENE/kernels/mk/

    lro: /scratch/jlaura/spice/lro-l-spice-6-v1.0/lrosp_1000/extras/mk/

    mdis: /data/spice/mess-e_v_h-spice-6-v1.0/messsp_1000/extras/mk

    mro: /data/spice/mro-m-spice-6-v1.0/mrosp_1000/extras/mk

    spice_root: /data/spice/

    Dawn spice directory: /data/spice/dawn-m_a-spice-6-v1.0/dawnsp_1000/extras/mk

%% Cell type:code id: tags:

``` python

# change to desired PDS3 image path

file_name = 'FC21A0039691_15231053805F1E.IMG'

# metakernels are furnsh-ed when entering the context (with block) with a driver instance

# most driver constructors simply accept an image path

with DawnFcPds3NaifSpiceDriver(file_name) as driver:

    # pass driver instance into formatter function

    usgscsmString = to_usgscsm(driver)

```

%% Cell type:markdown id: tags:

### Write ISD to disk

ALE formatter functions generally return bytes or a string that can be written out to disk. ALE's USGSCSM formatter function returns a JSON encoded string that can be written out using any JSON library.

USGSCSM requires the ISD to be colocated with the image file with a `.json` extension in place of the image extension.

%% Cell type:code id: tags:

``` python

# Load the json string into a dict

usgscsm_dict = json.loads(usgscsmString)

# Write the dict out to the associated file

json_file = os.path.splitext(file_name)[0] + '.json'

# Save off the json and read it back in to check if

# the json exists and was formatted correctly

with open(json_file, 'w') as fp:

    json.dump(usgscsm_dict, fp)

with open(json_file, 'r') as fp:

    usgscsm_dict = json.load(fp)

usgscsm_dict.keys()

```

%% Output

    dict_keys(['radii', 'sensor_position', 'sun_position', 'sensor_orientation', 'detector_sample_summing', 'detector_line_summing', 'focal_length_model', 'detector_center', 'starting_detector_line', 'starting_detector_sample', 'focal2pixel_lines', 'focal2pixel_samples', 'optical_distortion', 'image_lines', 'image_samples', 'name_platform', 'name_sensor', 'reference_height', 'name_model', 'center_ephemeris_time'])

%% Cell type:code id: tags:

``` python

```

%% Cell type:markdown id: tags:

# Writing out a USGSCSM ISD from an ISIS ideal camera image

%% Cell type:code id: tags:

``` python

import os

import json

import ale

from ale.drivers.isis_ideal_drivers import IdealLsIsisLabelIsisSpiceDriver

from ale.formatters.usgscsm_formatter import to_usgscsm

```

%% Cell type:markdown id: tags:

## Instantiating an ALE driver

ALE drivers are objects that define how to acquire common ISD keys from an input image format, in this case we are reading in an ISIS ideal line scan image using updated, attached exterior orientation data. These driver objects are short-lived and are input to a formatter function that consumes the API to create a serializable file format. `ale.formatters` contains available formatter functions.

ALE has a two step process for writing out an ISD: 1. Instantiate your driver (in this case `IdealLsIsisLabelIsisSpiceDriver`) within a context and 2. pass the driver object into a formatter (in this case, `to_usgscsm`).

Requirements:

 * An ISIS ideal line scan image (e.g. a deijjtered HiRISE image, an undistorted HRSC image, or any linescan image processed through [noproj](https://isis.astrogeology.usgs.gov/Application/presentation/Tabbed/noproj/noproj.html))

 * A conda environment with ALE installed into it usisng the `conda install` command or created using the environment.yml file at the base of ALE.

%% Cell type:code id: tags:

``` python

# change to desired PDS3 image path

file_name = '/Users/jmapel/ale/ESP_016076_2175_REDmos_hijitreged.balance.noproj.8bit.cub'

from ale.transformation import FrameChain, create_rotations

# metakernels are furnished when entering the context (with block) with a driver instance

# most driver constructors simply accept an image path

with IdealLsIsisLabelIsisSpiceDriver(file_name) as driver:

    usgscsmString = to_usgscsm(driver)

```

%% Cell type:markdown id: tags:

### Write ISD to disk

ALE formatter functions generally return bytes or a string that can be written out to disk. ALE's USGSCSM formatter function returns a JSON encoded string that can be written out using any JSON library.

USGSCSM requires the ISD to be colocated with the image file with a `.json` extension in place of the image extension.

%% Cell type:code id: tags:

``` python

# Load the json string into a dict

usgscsm_dict = json.loads(usgscsmString)

# Write the dict out to the associated file

json_file = os.path.splitext(file_name)[0] + '.json'

# Save off the json and read it back in to check if

# the json exists and was formatted correctly

with open(json_file, 'w') as fp:

    json.dump(usgscsm_dict, fp)

with open(json_file, 'r') as fp:

    usgscsm_dict = json.load(fp)

usgscsm_dict.keys()

```

%% Output

    dict_keys(['radii', 'sensor_position', 'sun_position', 'sensor_orientation', 'detector_sample_summing', 'detector_line_summing', 'focal_length_model', 'detector_center', 'starting_detector_line', 'starting_detector_sample', 'focal2pixel_lines', 'focal2pixel_samples', 'optical_distortion', 'image_lines', 'image_samples', 'name_platform', 'name_sensor', 'reference_height', 'name_model', 'interpolation_method', 'line_scan_rate', 'starting_ephemeris_time', 'center_ephemeris_time', 't0_ephemeris', 'dt_ephemeris', 't0_quaternion', 'dt_quaternion'])

%% Cell type:code id: tags:

``` python

```

%% Cell type:markdown id: tags:

# Writing out a USGSCSM ISD from a PDS3 LRO LROC NAC image

%% Cell type:code id: tags:

``` python

import ale

from ale.drivers.lro_drivers import LroLrocPds3LabelNaifSpiceDriver

from ale.formatters.usgscsm_formatter import to_usgscsm

import json

import os

```

%% Cell type:markdown id: tags:

## Instantiating an ALE driver

ALE drivers are objects that define how to acquire common ISD keys from an input image format, in this case we are reading in a PDS3 image using NAIF SPICE kernels for exterior orientation data. If the driver utilizes NAIF SPICE kernels, it is implemented as a [context manager](https://docs.python.org/3/reference/datamodel.html#context-managers) and will furnish metakernels when entering the context (i.e. when entering the `with` block) and free the metakernels on exit. This maintains the integrity of spicelib's internal data structures. These driver objects are short-lived and are input to a formatter function that consumes the API to create a serializable file format. `ale.formatters` contains available formatter functions.

The default config file is located at `ale/config.yml` and is copied into your home directory at `.ale/config.yml` on first use of the library. The config file can be modified using a text editor. `ale.config` is loaded into memory as a dictionary. It is used to find metakernels for different missions. For example, there is an entry for LRO that points to `/usgs/cpkgs/isis3/data/lro/kernels/mk/` by default. If you want to use your own metakernels, you will need to udpate this path. For example, if the metakernels are located in `/data/lrolrocnac/mk/` the LRO entry should be updated with this path. If you are using the default metakernels, then you do not need to update the path.

ALE has a two step process for writing out an ISD: 1. Instantiate your driver (in this case `LroLrocPds3LabelNaifSpiceDriver`) within a context and 2. pass the driver object into a formatter (in this case, `to_usgscsm`).

Requirements:

 * A PDS3 LRO LROC NAC image

 * NAIF metakernels installed

 * Config file path for LRO (ale.config.lro) pointing to LRO NAIF metakernel directory

 * A conda environment with ALE installed into it usisng the `conda install` command or created using the environment.yml file at the base of ALE.

%% Cell type:code id: tags:

``` python

# printing config displays the yaml formatted string

print(ale.config)

# config object is a dictionary so it has the same access patterns

print('LRO spice directory:', ale.config['lro'])

# updating config for new LRO path in this notebook

# Note: this will not change the path in `.ale/config.yml`. This change only lives in the notebook.

# ale.config['lro'] = '/data/lrolrocnac/mk/'

```

%% Output

    cassini: /usgs/cpkgs/isis3/data/cassini/kernels/mk/

    dawn: /data/spice/dawn-m_a-spice-6-v1.0/dawnsp_1000/extras/mk

    kaguya: /data/spice/SELENE/kernels/mk/

    lro: /scratch/jlaura/spice/lro-l-spice-6-v1.0/lrosp_1000/extras/mk/

    mdis: /data/spice/mess-e_v_h-spice-6-v1.0/messsp_1000/extras/mk

    mro: /data/spice/mro-m-spice-6-v1.0/mrosp_1000/extras/mk

    spice_root: /data/spice/

    LRO spice directory: /scratch/jlaura/spice/lro-l-spice-6-v1.0/lrosp_1000/extras/mk/

%% Cell type:code id: tags:

``` python

# change to desired PDS3 image path

fileName = 'M1142142198RE.IMG'

# metakernels are furnsh-ed when entering the context (with block) with a driver instance

# most driver constructors simply accept an image path

with LroLrocPds3LabelNaifSpiceDriver(fileName) as driver:

    # pass driver instance into formatter function

    usgscsmString = to_usgscsm(driver)

```

%% Cell type:markdown id: tags:

### Write ISD to disk

ALE formatter functions generally return bytes or a string that can be written out to disk. ALE's USGSCSM formatter function returns a JSON encoded string that can be written out using any JSON library.

USGSCSM requires the ISD to be colocated with the image file with a `.json` extension in place of the image extension.

%% Cell type:code id: tags:

``` python

# load the json encoded string ISD

usgscsm_dict = json.loads(usgscsmString)

# strip the image file extension and append .json

jsonFile = os.path.splitext(fileName)[0] + '.json'

# write to disk

with open(jsonFile, 'w') as fp:

    json.dump(usgscsm_dict, fp)

```

%% Cell type:markdown id: tags:

# Writing out a USGSCSM ISD from a PDS3 LRO LROC NAC image

%% Cell type:code id: tags:

``` python

import os

import json

import ale

from ale.drivers.mro_drivers import MroCtxPds3LabelNaifSpiceDriver

from ale.formatters.usgscsm_formatter import to_usgscsm

```

%% Cell type:markdown id: tags:

## Instantiating an ALE driver

ALE drivers are objects that define how to acquire common ISD keys from an input image format, in this case we are reading in a PDS3 image using NAIF SPICE kernels for exterior orientation data. If the driver utilizes NAIF SPICE kernels, it is implemented as a [context manager](https://docs.python.org/3/reference/datamodel.html#context-managers) and will furnish metakernels when entering the context (i.e. when entering the `with` block) and free the metakernels on exit. This maintains the integrity of spicelib's internal data structures. These driver objects are short-lived and are input to a formatter function that consumes the API to create a serializable file format. `ale.formatters` contains available formatter functions.

The default config file is located at `ale/config.yml` and is copied into your home directory at `.ale/config.yml` on first use of the library. The config file can be modified using a text editor. `ale.config` is loaded into memory as a dictionary. It is used to find metakernels for different missions. For example, there is an entry for MRO that points to `/usgs/cpkgs/isis3/data/mro/kernels/mk/` by default. If you want to use your own metakernels, you will need to udpate this path. For example, if the metakernels are located in `/data/ctxmro/mk/` the MRO entry should be updated with this path. If you are using the default metakernels, then you do not need to update the path.

ALE has a two step process for writing out an ISD: 1. Instantiate your driver (in this case `MroCtxPds3LabelNaifSpiceDriver`) within a context and 2. pass the driver object into a formatter (in this case, `to_usgscsm`).

Requirements:

 * A PDS3 CTX MRO image

 * NAIF metakernels installed

 * Config file path for MRO (ale.config.mro) pointing to MRO NAIF metakernel directory

 * A conda environment with ALE installed into it usisng the `conda install` command or created using the environment.yml file at the base of ALE.

%% Cell type:code id: tags:

``` python

# printing config displays the yaml formatted string

print(ale.config)

# config object is a dictionary so it has the same access patterns

print('MRO spice directory:', ale.config['mro'])

# updating config for new LRO path in this notebook

# Note: this will not change the path in `.ale/config.yml`. This change only lives in the notebook.

# ale.config['lro'] = '/data/lrolrocnac/mk/'

```

%% Output

    cassini: /usgs/cpkgs/isis3/data/cassini/kernels/mk/

    dawn: /data/spice/dawn-m_a-spice-6-v1.0/dawnsp_1000/extras/mk

    kaguya: /data/spice/SELENE/kernels/mk/

    lro: /scratch/jlaura/spice/lro-l-spice-6-v1.0/lrosp_1000/extras/mk/

    mdis: /data/spice/mess-e_v_h-spice-6-v1.0/messsp_1000/extras/mk

    mro: /data/spice/mro-m-spice-6-v1.0/mrosp_1000/extras/mk

    spice_root: /data/spice/

    MRO spice directory: /data/spice/mro-m-spice-6-v1.0/mrosp_1000/extras/mk

%% Cell type:code id: tags:

``` python

# change to desired PDS3 image path

file_name = '/home/acpaquette/F03_037064_1857_XN_05N218W.IMG'

# metakernels are furnsh-ed when entering the context (with block) with a driver instance

# most driver constructors simply accept an image path

with MroCtxPds3LabelNaifSpiceDriver(file_name) as driver:

    # pass driver instance into formatter function

    usgscsmString = to_usgscsm(driver)

```

%% Cell type:markdown id: tags:

### Write ISD to disk

ALE formatter functions generally return bytes or a string that can be written out to disk. ALE's USGSCSM formatter function returns a JSON encoded string that can be written out using any JSON library.

USGSCSM requires the ISD to be colocated with the image file with a `.json` extension in place of the image extension.

%% Cell type:code id: tags:

``` python

# Load the json string into a dict

usgscsm_dict = json.loads(usgscsmString)

# Write the dict out to the associated file

json_file = os.path.splitext(file_name)[0] + '.json'

# Save off the json and read it back in to check if

# the json exists and was formatted correctly

with open(json_file, 'w') as fp:

    json.dump(usgscsm_dict, fp)

with open(json_file, 'r') as fp:

    usgscsm_dict = json.load(fp)

usgscsm_dict.keys()

```

%% Output

    dict_keys(['radii', 'sensor_position', 'sun_position', 'sensor_orientation', 'detector_sample_summing', 'detector_line_summing', 'focal_length_model', 'detector_center', 'starting_detector_line', 'starting_detector_sample', 'focal2pixel_lines', 'focal2pixel_samples', 'optical_distortion', 'image_lines', 'image_samples', 'name_platform', 'name_sensor', 'reference_height', 'name_model', 'interpolation_method', 'line_scan_rate', 'starting_ephemeris_time', 'center_ephemeris_time', 't0_ephemeris', 'dt_ephemeris', 't0_quaternion', 'dt_quaternion'])

%% Cell type:code id: tags:

``` python

```