Merge pull request #13 from elliesch/master

Added License, Requirements.txt and Updated ReadMe file

LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2017, Ellianna Schwab, Kelle Cruz
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,25 +1,72 @@
 # UltracoolTypingKit
 Home for qualitative spectral typing GUI that follows the Cruz Method as proposed in <Cruz et al. (2017)>.
 Currently this GUI spectral types L field, L beta and L gamma brown dwarfs.
-This code is written in Python 3.6, and does not yet have functionality for Python 2.
+This code is written in Python 3.6, and does not yet have functionality for Python 2 and works with
+input fits files of NIR spectra.
 
 
-## Usage
+## Installation
+
+To install clone this repository:
+
+```bash
+$ git clone https://github.com/BDNYC/UltracoolTypingKit
+$ cd UltracoolTypingKit/
+$ mkdir new_types
+
+```
+
+UltracoolTypingKit (UTK) requires Python 3.5 to run properly. We recommend running in an environment to ensure usage of the correct version of Python and all the necessary modules.
+
+```bash
+$ conda create --name UTK python=3.5 ipython
+$ source activate UTK
+$ pip install -r requirements.txt
+
+``` 
 
 This code currently requires this directory tree to run properly:
 
 ```
+UltracoolTypingKit/
 ├── TypeFinder.py  
 ├── new_types/  
 │   └── saves selected spectral type image here  
-├── spectra/    
+├── spectra/  
+│   ├── store T0 and M9 spectral standards here   
 │   └── nir/  
 │       ├── store NIR spectra here  
 │       └── store NIR spectral standards (Table 9, Cruz et al. 2017) here    
 └── templates/  
     └── store Cruz2017_Templates.hdf5 here  
  ```
 
+
+## Usage
+
+
+### 1. Running UTK
+
+If you aren't already in the UTK environment, activate UTK.
+```bash
+$ source activate UTK
+```
+
+UTK relies on an interactive backend and works best with `TkAgg`. ipython pylab uses this as its default.
+
+```bash
+$ ipython --pylab
+
+```
+
+To run UTK on one spectrum, use the following input.
+
+```python
+from TypeFinder import *
+typing_kit("spectra/nir/spectra_file.fits")
+
+```
+
 To run many spectra consecutively, the following wrapper can be helpful.
 It will print out the file name and wait for the user to press enter before continuing.
 
@@ -34,25 +81,9 @@ for file in range(len(lines)):
    ...:     input("Press Enter to continue...")
 
 ```
-
-If you have the Cruz 2017 templates in ascii format, you can [download](.../blob/master/templates/Cruz2017_Templates.hdf5) the hdf5 file from this repository.
-You can also save an hdf5 file the first time you run Ultracool Typing Kit.
-
-```python
-from TypeFinder import*
-typing_kit("spectra/nir/somespectra", make_templates=True)
-
-```
-
-By default make_templates is false, and this input will raise an exception if Cruz2017_Templates.hdf5 already exists.
 
-
----
-
-
-### 1. Running the Program
-On running, this initial window will pop up, after about 10 seconds:
-<img src="https://raw.githubusercontent.com/elliesch/UltracoolTypingKit/master/opengrid.png" width="750">
+After about 10 seconds, this initial window will pop up:
+<img src="https://raw.githubusercontent.com/elliesch/UltracoolTypingKit/master/resources/opengrid.png" width="750">
 
 Your input spectra will be shown in black, over the Cruz et al. (2017) J-H-K band templates shown in red.
 The initial grid shows each spectral type band-by-band.
@@ -80,22 +111,31 @@ For example for an L2-gamma press:
 <kbd>alt</kbd> + <kbd>1</kbd>
 
 After keying in your selection, a window centered on your spectral type will pop up:
- ![Grid of Spectral Type Selection](https://raw.githubusercontent.com/elliesch/UltracoolTypingKit/master/L3.png)
+ ![Grid of Spectral Type Selection](https://raw.githubusercontent.com/elliesch/UltracoolTypingKit/master/resources/L3.png)
 
 This grid shows your selected spectral type bracketed by it's neighboring types, both band-by-band and across
 the entire NIR spectrum at once in the right-hand column, following the same color scheme as the initial grid. 
 The templates used in for the entire NIR spectrum follow the templates specified in Cruz et al. (2017).
 
 
 
+### 3. Viewing Alternate Spectral Types
+If you keyed in a spectral type and you want to see a different one, press <kbd>q</kbd> to close the window containing your initial selection and to return to the initial grid window.
+
+
+
+
+### 4. Saving a Spectral Type
+Once you have settled on a spectral type, you can save the image of the selected type by pressing <kbd>w</kbd>. This will create a csv file in the folder new_types/ that will save your input file name in column 1 and your selected spectral type in column 2. The csv file is named XX-XX-XXXX_SpecTypes.csv, XX represents today's date in day-month-year format. As you spectral type more objects, they will append as new rows to the csv file.
+
+Pressing <kbd>w</kbd> will also save an image of the current plot view as a .png to the new_types/ folder with the name of your input spectrum file and your selected spectral type appended after an underscore, for example, like this for an L0: InputFileName_L0.png
+
+You can then close the selection window by pressing <kbd>q</kbd> and then the grid window by again pressing <kbd>q</kbd>.
 
-### 3. Saving Selected Spectral Type
-Currently the code automatically saves an image of your selection into the new_types folder. We are in the process 
-of updating it so that you can select whether you would prefer to save or see another type.
 
 
 
 ## Citation
-Copyright 2017 Ellianna Schwab and collaborators
+Copyright 2017 Ellianna Schwab, Kelle Cruz
 
 If you make use of this code, please cite Cruz et al. (2017) and the zenodo DOI for the code, coming soon!

TypeFinder.py

@@ -1,10 +1,26 @@
 import numpy as np
 import matplotlib.pyplot as plt
-# from pylab import *
 from collections import defaultdict
 from astropy.io import fits
 from astropy.io import ascii
 from astropy.table import Table, Column
+import os
+import time
+
+plt.rcParams['keymap.save'] = ''
+
+'''
+Ellianna Schwab, Kelle Cruz
+
+TypeFinder.py contains typing_kit, which provides plots to qualitatively spectral type L-type brown dwarfs in NIR regime.
+Typing methods are taken from Cruz et al. 2017 and offer comparison to NIR spectral standards.
+
+To use input path to file_name in a string. A band-by-band grid of Cruz et al 2017 templates
+will be overplotted with the target spectrum. To compare to the NIR spectral standards as well, 
+key in the spectral type number, '0' - '8'. 
+Cruz et al. 2017 templates are shown band-by-band followed by a comparison to the overall NIR spectrum of NIR 
+spectral standards as defined in Table 9 of Cruz et al 2017.
+'''
 
 class Data:
 
@@ -136,6 +152,7 @@ def __init__(self, file_name, type_number, NIR_standards): #This defines often r
         #Define the other variables
         self.type_number = type_number
         self.NIR_standards = NIR_standards
+        self.file_name = file_name
 
 
     def bracketed_plot(self, gravity_type): #This is for bracketed plots that are not first or last
@@ -189,7 +206,7 @@ def bracketed_plot(self, gravity_type): #This is for bracketed plots that are no
                 axes2[jj, 2].axis('off')
 
 
-                #All Together Now! This is where the Kirkpatrick 10 one comes in.
+                #All Together Now! This is where the spectral standard comes in.
                 temp_hdulist = fits.open(self.NIR_standards[ii])
                 temp_spectrum = temp_hdulist[0]
                 temp_wavelength = temp_spectrum.data[0]
@@ -210,7 +227,16 @@ def bracketed_plot(self, gravity_type): #This is for bracketed plots that are no
                 axes2[jj, 3].plot(self.wavelength, self.norm_flux, c='k')
                 axes2[jj, 3].axis('off')
 
-        # fig2.savefig('new_types/' + self.file_name[12:-5] + r'_L{}'.format(self.type_number))
+        save_name = 'new_types/' + self.file_name[12:-5] + r'_L{}{}'.format(self.type_number, gravity_type)
+
+        def save_figure(event):
+            if event.key == 'w':
+                plt.savefig(save_name)
+                save_types(self.file_name, self.type_number, gravity_type)
+
+        fig2.canvas.mpl_connect('key_press_event', manipulate_figure)
+        fig2.canvas.mpl_connect('key_press_event', save_figure)
+
 
     def first_bracketed_plot(self, gravity_type): 
 
@@ -287,7 +313,7 @@ def first_bracketed_plot(self, gravity_type):
                 axes2[jj, 2].axis('off')
 
 
-                #All Together Now! This is where the Kirkpatrick 10 one comes in.
+                #All Together Now! This is where the spectral standard comes in.
                 temp_hdulist = fits.open(self.NIR_standards[ii])
                 temp_spectrum = temp_hdulist[0]
                 temp_wavelength = temp_spectrum.data[0]
@@ -308,7 +334,16 @@ def first_bracketed_plot(self, gravity_type):
                 axes2[jj, 3].plot(self.wavelength, self.norm_flux, c='k')
                 axes2[jj, 3].axis('off')
 
-        # fig2.savefig('new_types/' + self.file_name[12:-5] + r'_L{}'.format(self.type_number))
+        save_name = 'new_types/' + self.file_name[12:-5] + r'_L{}{}'.format(self.type_number, gravity_type)
+
+        def save_figure(event):
+            if event.key == 'w':
+                plt.savefig(save_name)
+                save_types(self.file_name, self.type_number, gravity_type)
+
+        fig2.canvas.mpl_connect('key_press_event', manipulate_figure)
+        fig2.canvas.mpl_connect('key_press_event', save_figure)
+
 
     def last_bracketed_plot(self, gravity_type):
 
@@ -362,7 +397,7 @@ def last_bracketed_plot(self, gravity_type):
                 axes2[jj, 2].axis('off')
 
 
-                #All Together Now! This is where the Kirkpatrick 10 one comes in.
+                #All Together Now! This is where the spectral standard comes in.
                 temp_hdulist = fits.open(self.NIR_standards[jj])
                 temp_spectrum = temp_hdulist[0]
                 temp_wavelength = temp_spectrum.data[0]
@@ -405,10 +440,47 @@ def last_bracketed_plot(self, gravity_type):
         axes2[2, 3].plot(temp_wavelength, temp_norm_flux, c='red')
         axes2[2, 3].plot(self.wavelength, self.norm_flux, c='k')
         axes2[2, 3].axis('off')
-
-        # fig2.savefig('new_types/' + self.file_name[12:-5] + r'_L{}'.format(self.type_number))
 
+        save_name = 'new_types/' + self.file_name[12:-5] + r'_L{}{}'.format(self.type_number, gravity_type)
+
+        def save_figure(event):
+            if event.key == 'w':
+                plt.savefig(save_name)
+                save_types(self.file_name, self.type_number, gravity_type)
+
+        fig2.canvas.mpl_connect('key_press_event', manipulate_figure)
+        fig2.canvas.mpl_connect('key_press_event', save_figure)
+
+
+def save_types(file_name, type_number, gravity_type):
 
+    '''
+    saves output csv file with filename in column 1, and spectral type in column 2
+    '''
+
+    now_date = time.strftime("%d-%m-%Y")
+
+    if os.path.isfile(r'new_types/{}_SpecTypes.csv'.format(now_date)) == True :
+        f = open(r'new_types/{}_SpecTypes.csv'.format(now_date), 'a')
+        f.write(r'{}, L{}{}'.format(file_name[12:], type_number, gravity_type))
+        f.write('\n')
+        f.close()
+
+    else :
+        f = open(r'new_types/{}_SpecTypes.csv'.format(now_date), 'w')
+        f.write(r'{}, L{}{}'.format(file_name[12:], type_number, gravity_type))
+        f.write('\n')        
+        f.close()
+
+
+def manipulate_figure(event):
+
+    '''
+    closes selected plot window when q is pressed on the keyboard
+    '''
+
+    if event.key == 'q':
+        plt.close(event.canvas.figure)
 
 ### Function definition
 def typing_kit(file_name, make_templates=False) :
@@ -417,17 +489,18 @@ def typing_kit(file_name, make_templates=False) :
     Ellianna Schwab, Kelle Cruz
 
     typing_kit provides plots to qualitatively spectral type L-type brown dwarfs in NIR regime.
-    Typing methods are taken from Cruz et al. 2017 and offer comparison to Kirkpatrick 2010 typing templates.
+    Typing methods are taken from Cruz et al. 2017 and offer comparison to NIR spectral standards.
 
     To use input path to file_name in a string. A band-by-band grid of Cruz et al 2017 templates
-    will be overplotted with the target spectrum. To compare to Kirkpatrick 2010, key in the spectral type
-    number, '0' - '8'. Cruz et al. 2017 templates are shown band-by-band followed by Kirkpatrick 2010
-    templates of the overall NIR spectrum.
+    will be overplotted with the target spectrum. To compare to the NIR spectral standards as well, 
+    key in the spectral type number, '0' - '8'. 
+    Cruz et al. 2017 templates are shown band-by-band followed by a comparison to the overall NIR spectrum of NIR 
+    spectral standards as defined in Table 9 of Cruz et al 2017.
     '''
 
 
     ##===============
-    #Optional Section to Translate Templates to HDF5
+    #If Necessary, Convert Ascii templates to HDF5
     ##===============
 
     if make_templates == True:
@@ -698,7 +771,7 @@ def on_key_press(event):
 
 
         #Raise an error message if any other key is pressed
-        elif event.key in 'abcdefghijklmnopqrstuvwxyz`-=[];,.':
+        elif event.key in 'abcdefghijklmnoprstuvxyz`-=[];,.':
             raise Exception('Invalid Key. Try any int in range(10) for field, ctrl + int in range(1) for beta, or alt + int in range(4) for gamma.')    
 
 
@@ -709,4 +782,10 @@ def on_key_press(event):
     fig1.canvas.draw()
 
     fig1.canvas.mpl_disconnect(fig1.canvas.manager.key_press_handler_id)
-    fig1.canvas.mpl_connect('key_press_event', on_key_press) #This leaves it open to a second try
+    fig1.canvas.mpl_connect('key_press_event', on_key_press) #This leaves it open to a second try
+
+    ##==============
+    #Close the plot via the keyboard
+    ##==============
+
+    fig1.canvas.mpl_connect('key_press_event', manipulate_figure)

requirements.txt

@@ -0,0 +1,4 @@
+numpy==1.11.1
+matplotlib==1.5.3
+astropy==1.2.1
+h5py