Merge pull request #19 from LSSTDESC/#16

#16
LSSTDESC · Apr 5, 2019 · ace42fd · ace42fd
2 parents 99c8a0b + 4ee33cc
commit ace42fd
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diff --git a/README.md b/README.md
@@ -7,17 +7,29 @@ Tools to create blend catalogs, produce training samples and implement blending
 Documentation can be found at https://blendingtoolkit.readthedocs.io/en/latest/
 
 ## Workflow
-- Step 1: import raw catalogs from CatSim or the DC2 catalogs
-- Step 2: modify those catalogs to create catalogs of (multiple) blends and explore joint distributions (separation, magnitude difference)
-- Step 3: generate PSF-convolved images and perform data augmentation
-- Step 4: train deep-learning algorthms to do various blending-related tasks such as detection, segmentation, deblending and measurements
-- Step 5: test algorithms with a set of low- and high-level performance metrics
+<img src="docs/source/images/flow_chart.png" alt="btk workflow" width="450"/>
 
 
-## Input Catalog
-- Catsim like catalogs and pre-processed WeakLensingDeblending catlogs can be found [here](https://weaklensingdeblending.readthedocs.io/en/latest/products.html)
+## Running BlendingToolKit
+- BlendingToolKit (btk) requires an input catalog that contains information required to simulate galaxies and blends.
+This repository includes sample input catalogs with small number of galaxies that can be used to draw blend images with btk. See [tutorials](https://github.com/LSSTDESC/BlendingToolKit/tree/master/notebooks) to learn how to run btk with these catalogs.
+- Catalog corresponding to one square degree sky and pre-processed WeakLensingDeblending catalogs can be downloaded from [here](https://stanford.app.box.com/s/s1nzjlinejpqandudjyykjejyxtgylbk).
 
-## Useful tools
+## Requirements
+The code is intended to run in python >=3.6.
+To run btk you need to install
 - [WeakLensingDeblending](https://github.com/LSSTDESC/WeakLensingDeblending)
 - [GalSim](https://github.com/GalSim-developers/GalSim/)
-- [Scarlet](https://github.com/fred3m/scarlet/)
+- numpy
+- astropy
+- fitsio
+- scipy
+- lmfit
+
+More detailed installation instructions can be found [here](https://blendingtoolkit.readthedocs.io/en/latest/install.html)
+
+### Optional
+The tutorials include examples of using btk with some packages like
+- [scarlet](https://github.com/fred3m/scarlet/) (multi-band deblender)
+- [sep](https://sep.readthedocs.io/en/v1.0.x/index.html)(Source Extraction and Photometry)
+- [lsst](https://pipelines.lsst.io) science pipeline
diff --git a/btk/create_blend_generator.py b/btk/create_blend_generator.py
@@ -1,4 +1,5 @@
 import numpy as np
+import warnings
 
 
 def get_random_center_shift(Args, number_of_objects, maxshift=None):
@@ -72,9 +73,12 @@ def generate(Args, catalog, sampling_function=None):
                 blend_catalog = default_sampling(Args, catalog)
                 if Args.verbose:
                     print("Default random sampling of objects from catalog")
-            np.testing.assert_array_less(
-                len(blend_catalog) - 1, Args.max_number, "Number of objects"
-                " per blend must be less than max_number: {0} <= {1}".format(
-                    len(blend_catalog), Args.max_number))
+            if len(blend_catalog) > Args.max_number:
+                raise ValueError("Number of objects per blend must be less \
+                    than max_number: {0} <= {1}".format(
+                        len(blend_catalog), Args.max_number))
+            if (np.any(blend_catalog['ra'] > Args.stamp_size/2.) or
+                    np.any(blend_catalog['dec'] > Args.stamp_size/2.)):
+                warnings.warn('Object center lies outside the stamp')
             blend_catalogs.append(blend_catalog)
         yield blend_catalogs
diff --git a/btk/create_observing_generator.py b/btk/create_observing_generator.py
@@ -44,5 +44,13 @@ def generate(Args, obs_function=None):
             descwl_survey = descwl.survey.Survey(no_analysis=True,
                                                  survey_name=Args.survey_name,
                                                  filter_band=band, **survey)
+            if descwl_survey.pixel_scale != Args.pixel_scale:
+                raise ValueError("observing condition pixel scale does not \
+                    match input pixel scale: {0} == {1}".format(
+                        descwl_survey.pixel_scale, Args.pixel_scale))
+            if descwl_survey.filter_band != band:
+                raise ValueError("observing condition band does not \
+                    match input band: {0} == {1}".format(
+                        descwl_survey.filter_band, band))
             observing_generator.append(descwl_survey)
         yield observing_generator
diff --git a/docs/api/btk.compute_metrics.rst b/docs/api/btk.compute_metrics.rst
diff --git a/docs/api/btk.config.rst b/docs/api/btk.config.rst
diff --git a/docs/api/btk.create_blend_generator.rst b/docs/api/btk.create_blend_generator.rst
diff --git a/docs/api/btk.create_observing_generator.rst b/docs/api/btk.create_observing_generator.rst
diff --git a/docs/api/btk.draw_blends.rst b/docs/api/btk.draw_blends.rst
diff --git a/docs/api/btk.get_input_catalog.rst b/docs/api/btk.get_input_catalog.rst
diff --git a/docs/api/btk.measure.rst b/docs/api/btk.measure.rst
diff --git a/docs/api/btk.rst b/docs/api/btk.rst
diff --git a/docs/api/btk.temp.rst b/docs/api/btk.temp.rst
diff --git a/docs/api/btk.test_btk.rst b/docs/api/btk.test_btk.rst
diff --git a/docs/api/btk.utils.rst b/docs/api/btk.utils.rst
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -28,6 +28,6 @@ Evaluate Metrics with btk (*evaluate_metrics.ipynb*)
 ----------------------------------------------------
 This `notebook <https://github.com/LSSTDESC/BlendingToolKit/blob/%2315/notebooks/evaluate_metrics.ipynb>`_ shows how to test performance of different detection/deblending/measurement algorithms. At present this only assesses detection performance by returning the number of objects correctly detected, number undetected and number of spurious detections.
 
-5. Draw blends (*create_blend_generator*): Simulates scene of overlapping objects, convolved by PSF and with pixel noise (option set in *config*). Scene image is generated in each observing band. Isolated image of each object is also drawn without pixel contributions from other objects, in each band.
+Draw blends (*create_blend_generator*): Simulates scene of overlapping objects, convolved by PSF and with pixel noise (option set in *config*). Scene image is generated in each observing band. Isolated image of each object is also drawn without pixel contributions from other objects, in each band.
 
 
diff --git a/docs/source/user_guide.rst b/docs/source/user_guide.rst
@@ -4,7 +4,7 @@ User Guide
 This document gives a detailed look into the work-flow of *BlendingToolKit* (btk). For a quick tutorial on how to run btk, see the JuPyter notebook tutorials :doc:`here </tutorials>`. This page is especially useful if you plan on using btk with your own detection/deblending/measurement algorithm.
 
 
-The work-flow of btk is shown below
+The workflow of btk is shown below
 
 .. image:: images/flow_chart.png
    :align: center

diff --git a/notebooks/custom_sampling_function.ipynb b/notebooks/custom_sampling_function.ipynb
diff --git a/notebooks/run_basic.ipynb b/notebooks/run_basic.ipynb
@@ -14,27 +14,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2019-04-01T21:21:30.475879Z",
-     "start_time": "2019-04-01T21:21:26.952434Z"
+     "end_time": "2019-04-04T22:45:18.600782Z",
+     "start_time": "2019-04-04T22:45:15.057320Z"
     }
    },
    "outputs": [],
    "source": [
-    "import os\n",
-    "import numpy as np\n",
-    "import galsim\n",
-    "import sys\n",
-    "import descwl\n",
-    "import argparse\n",
-    "\n",
-    "import copy\n",
     "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
+    "import os\n",
+    "import sys\n",
+    "import numpy as np\n",
     "\n",
-    "#importing scarlet to make RGB images\n",
+    "#import scarlet.display to plot RGB images if scarelt is installed\n",
     "if 'scarlet' in sys.modules:\n",
     "    import scarlet.display\n",
     "\n",
@@ -45,21 +40,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2019-04-01T21:21:30.563261Z",
-     "start_time": "2019-04-01T21:21:30.530562Z"
+     "end_time": "2019-04-04T22:45:18.635367Z",
+     "start_time": "2019-04-04T22:45:18.609382Z"
     },
     "code_folding": [
-     0,
-     13,
-     29,
-     67
+     1,
+     14,
+     31,
+     69
     ]
    },
    "outputs": [],
    "source": [
+    "# Functions helpful for plotting blend images\n",
     "def get_rgb(image, min_val=None, max_val=None):\n",
     "    \"\"\"Basic function to normalize 3 band input image to rgb 0-255 image\"\"\"\n",
     "    assert image.shape[0] == 3, \"must be 3 channel in dimension 1\"\n",