Merge branch 'master' into fix/brian/nonascii-html-xmodule

brew-formulas.txt

-readline 
-sqlite 
-gdbm 
-pkg-config 
-gfortran 
-python 
-yuicompressor 
+readline
+sqlite
+gdbm
+pkg-config
+gfortran
+python
+yuicompressor
 node
 graphviz
 mysql
+geos

common/lib/capa/capa/capa_problem.py

@@ -33,6 +33,7 @@ from xml.sax.saxutils import unescape
 import chem
 import chem.chemcalc
 import chem.chemtools
+import chem.miller
 
 import calc
 from correctmap import CorrectMap
@@ -67,7 +68,8 @@ global_context = {'random': random,
                   'calc': calc,
                   'eia': eia,
                   'chemcalc': chem.chemcalc,
-                  'chemtools': chem.chemtools}
+                  'chemtools': chem.chemtools,
+                  'miller': chem.miller}
 
 # These should be removed from HTML output, including all subelements
 html_problem_semantics = ["codeparam", "responseparam", "answer", "script", "hintgroup"]

common/lib/capa/capa/chem/miller.py

+""" Calculation of Miller indices """
+
+import numpy as np
+import math
+import fractions as fr
+import decimal
+import json
+
+
+def lcm(a, b):
+    """
+    Returns least common multiple of a, b
+
+    Args:
+        a, b: floats
+
+    Returns:
+        float
+    """
+    return a * b / fr.gcd(a, b)
+
+
+def segment_to_fraction(distance):
+    """
+    Converts lengths of which the plane cuts the axes to fraction.
+
+    Tries convert distance to closest nicest fraction with denominator less or
+    equal than 10. It is
+    purely for simplicity and clearance of learning purposes. Jenny: 'In typical
+    courses students usually do not encounter indices any higher than 6'.
+
+    If distance is not a number (numpy nan), it means that plane is parallel to
+    axis or contains it. Inverted fraction to nan (nan is 1/0) = 0 / 1 is
+    returned
+
+    Generally (special cases):
+
+    a) if distance is smaller than some constant, i.g. 0.01011,
+    than fraction's denominator usually much greater than 10.
+
+    b) Also, if student will set point on 0.66 -> 1/3, so it is 333 plane,
+    But if he will slightly move the mouse and click on 0.65 -> it will be
+    (16,15,16) plane. That's why we are doing adjustments for points coordinates,
+    to the closest tick, tick + tick / 2 value. And now UI sends to server only
+    values multiple to 0.05  (half of tick). Same rounding is implemented for
+    unittests.
+
+    But if one will want to calculate miller indices with exact coordinates and
+    with nice fractions (which produce small Miller indices), he may want shift
+    to new origin if segments are like S = (0.015, > 0.05, >0.05) - close to zero
+    in one coordinate. He may update S to (0, >0.05, >0.05) and shift origin.
+    In this way he can recieve nice small fractions. Also there is can be
+    degenerated case when S = (0.015, 0.012, >0.05) - if update S to (0, 0, >0.05) -
+    it is a line. This case  should be considered separately. Small nice Miller
+    numbers and possibility to create very small segments can not be implemented
+    at same time).
+
+
+    Args:
+        distance: float distance that plane cuts on axis, it must not be 0.
+        Distance is multiple of 0.05.
+
+    Returns:
+         Inverted fraction.
+         0 / 1 if distance is nan
+
+    """
+    if np.isnan(distance):
+        return fr.Fraction(0, 1)
+    else:
+        fract = fr.Fraction(distance).limit_denominator(10)
+        return fr.Fraction(fract.denominator, fract.numerator)
+
+
+def sub_miller(segments):
+    '''
+    Calculates Miller indices from segments.
+
+    Algorithm:
+
+    1. Obtain inverted fraction from segments
+
+    2. Find common denominator of inverted fractions
+
+    3. Lead fractions to common denominator and throws denominator away.
+
+    4. Return obtained values.
+
+    Args:
+        List of 3 floats, meaning distances that plane cuts on x, y, z axes.
+        Any float not equals zero, it means that plane does not intersect origin,
+        i. e. shift of origin has already been done.
+
+    Returns:
+        String that represents Miller indices, e.g: (-6,3,-6) or (2,2,2)
+    '''
+    fracts = [segment_to_fraction(segment) for segment in segments]
+    common_denominator = reduce(lcm, [fract.denominator for fract in fracts])
+    miller = ([fract.numerator * math.fabs(common_denominator) /
+                                fract.denominator for fract in fracts])
+    return'(' + ','.join(map(str, map(decimal.Decimal, miller))) + ')'
+
+
+def miller(points):
+    """
+    Calculates Miller indices from points.
+
+    Algorithm:
+
+    1. Calculate normal vector to a plane that goes trough all points.
+
+    2. Set origin.
+
+    3. Create Cartesian coordinate system (Ccs).
+
+    4. Find the lengths of segments of which the plane cuts the axes. Equation
+       of a line for axes: Origin + (Coordinate_vector - Origin) * parameter.
+
+    5. If plane goes trough Origin:
+
+       a) Find new random origin: find unit cube vertex, not crossed by a plane.
+
+       b) Repeat 2-4.
+
+       c) Fix signs of segments after Origin shift. This means to consider
+          original directions of axes. I.g.: Origin was 0,0,0 and became
+          new_origin. If new_origin has same Y coordinate as Origin, then segment
+          does not change its sign. But if new_origin has another Y coordinate than
+          origin (was 0, became 1), than segment has to change its sign (it now
+          lies on negative side of Y axis). New Origin 0 value of X or Y or Z
+          coordinate means that segment does not change sign, 1 value -> does
+          change. So new sign  is (1 - 2 * new_origin): 0 -> 1, 1 -> -1
+
+    6. Run function that calculates miller indices from segments.
+
+    Args:
+        List of points. Each point is list of float coordinates. Order of
+        coordinates in point's list: x, y, z. Points are different!
+
+    Returns:
+        String that represents Miller indices, e.g: (-6,3,-6) or (2,2,2)
+    """
+
+    N = np.cross(points[1] - points[0], points[2] - points[0])
+    O = np.array([0, 0, 0])
+    P = points[0]  # point of plane
+    Ccs = map(np.array, [[1.0, 0, 0], [0, 1.0, 0], [0, 0, 1.0]])
+    segments = ([np.dot(P - O, N) / np.dot(ort, N) if np.dot(ort, N) != 0 else
+                                            np.nan for ort in Ccs])
+    if any(x == 0 for x in segments):  # Plane goes through origin.
+        vertices = [  # top:
+                    np.array([1.0, 1.0, 1.0]),
+                    np.array([0.0, 0.0, 1.0]),
+                    np.array([1.0, 0.0, 1.0]),
+                    np.array([0.0, 1.0, 1.0]),
+                    # bottom, except 0,0,0:
+                    np.array([1.0, 0.0, 0.0]),
+                    np.array([0.0, 1.0, 0.0]),
+                    np.array([1.0, 1.0, 1.0]),
+                ]
+        for vertex in vertices:
+            if np.dot(vertex - O, N) != 0:  # vertex not in plane
+                new_origin = vertex
+                break
+        # obtain new axes with center in new origin
+        X = np.array([1 - new_origin[0], new_origin[1], new_origin[2]])
+        Y = np.array([new_origin[0], 1 - new_origin[1], new_origin[2]])
+        Z = np.array([new_origin[0], new_origin[1], 1 - new_origin[2]])
+        new_Ccs = [X - new_origin, Y - new_origin, Z - new_origin]
+        segments = ([np.dot(P - new_origin, N) / np.dot(ort, N) if
+                    np.dot(ort, N) != 0 else np.nan for ort in new_Ccs])
+        # fix signs of indices: 0 -> 1, 1 -> -1 (
+        segments = (1 - 2 * new_origin) * segments
+
+    return sub_miller(segments)
+
+
+def grade(user_input, correct_answer):
+    '''
+    Grade crystallography problem.
+
+    Returns true if lattices are the same and Miller indices are same or minus
+    same. E.g. (2,2,2) = (2, 2, 2) or (-2, -2, -2). Because sign depends only
+    on student's selection of origin.
+
+    Args:
+        user_input, correct_answer: json. Format:
+
+        user_input: {"lattice":"sc","points":[["0.77","0.00","1.00"],
+        ["0.78","1.00","0.00"],["0.00","1.00","0.72"]]}
+
+        correct_answer: {'miller': '(00-1)', 'lattice': 'bcc'}
+
+        "lattice" is one of: "", "sc", "bcc", "fcc"
+
+    Returns:
+        True or false.
+    '''
+    def negative(m):
+        """
+        Change sign of Miller indices.
+
+        Args:
+            m: string with meaning of Miller indices. E.g.:
+            (-6,3,-6) -> (6, -3, 6)
+
+        Returns:
+            String with changed signs.
+        """
+        output = ''
+        i = 1
+        while i in range(1, len(m) - 1):
+            if m[i] in (',', ' '):
+                output += m[i]
+            elif m[i] not in ('-', '0'):
+                output += '-' + m[i]
+            elif m[i] == '0':
+                output += m[i]
+            else:
+                i += 1
+                output += m[i]
+            i += 1
+        return '(' + output + ')'
+
+    def round0_25(point):
+        """
+        Rounds point coordinates to closest 0.5 value.
+
+        Args:
+            point: list of float coordinates. Order of coordinates: x, y, z.
+
+        Returns:
+            list of coordinates rounded to closes 0.5 value
+        """
+        rounded_points = []
+        for coord in point:
+            base = math.floor(coord * 10)
+            fractional_part = (coord * 10 - base)
+            aliquot0_25 = math.floor(fractional_part / 0.25)
+            if aliquot0_25 == 0.0:
+                rounded_points.append(base / 10)
+            if aliquot0_25 in (1.0, 2.0):
+                rounded_points.append(base / 10 + 0.05)
+            if aliquot0_25 == 3.0:
+                rounded_points.append(base / 10 + 0.1)
+        return rounded_points
+
+    user_answer = json.loads(user_input)
+
+    if user_answer['lattice'] != correct_answer['lattice']:
+        return False
+
+    points = [map(float, p) for p in user_answer['points']]
+
+    if len(points) < 3:
+        return False
+
+    # round point to closes 0.05 value
+    points = [round0_25(point) for point in points]
+
+    points = [np.array(point) for point in points]
+    # print miller(points), (correct_answer['miller'].replace(' ', ''),
+    #     negative(correct_answer['miller']).replace(' ', ''))
+    if miller(points) in (correct_answer['miller'].replace(' ', ''), negative(correct_answer['miller']).replace(' ', '')):
+        return True
+
+    return False

common/lib/capa/capa/inputtypes.py

@@ -671,18 +671,15 @@ class Crystallography(InputTypeBase):
         """
         Note: height, width are required.
         """
-        return [Attribute('size', None),
-                Attribute('height'),
+        return [Attribute('height'),
                 Attribute('width'),
-
-                # can probably be removed (textline should prob be always-hidden)
-                Attribute('hidden', ''),
                 ]
 
 registry.register(Crystallography)
 
 # -------------------------------------------------------------------------
 
+
 class VseprInput(InputTypeBase):
     """
     Input for molecular geometry--show possible structures, let student

common/lib/capa/capa/responsetypes.py

@@ -23,6 +23,7 @@ import abc
 import os
 import subprocess
 import xml.sax.saxutils as saxutils
+from shapely.geometry import Point, MultiPoint
 
 # specific library imports
 from calc import evaluator, UndefinedVariable
@@ -1717,15 +1718,38 @@ class ImageResponse(LoncapaResponse):
     which produces an [x,y] coordinate pair.  The click is correct if it falls
     within a region specified.  This region is a union of rectangles.
 
-    Lon-CAPA requires that each <imageresponse> has a <foilgroup> inside it.  That
-    doesn't make sense to me (Ike).  Instead, let's have it such that <imageresponse>
-    should contain one or more <imageinput> stanzas. Each <imageinput> should specify
-    a rectangle, given as an attribute, defining the correct answer.
+    Lon-CAPA requires that each <imageresponse> has a <foilgroup> inside it.
+    That doesn't make sense to me (Ike).  Instead, let's have it such that
+    <imageresponse> should contain one or more <imageinput> stanzas.
+    Each <imageinput> should specify a rectangle(s) or region(s), given as an
+    attribute, defining the correct answer.
+
+    <imageinput src="/static/images/Lecture2/S2_p04.png" width="811" height="610"
+    rectangle="(10,10)-(20,30);(12,12)-(40,60)"
+    regions="[[[10,10], [20,30], [40, 10]], [[100,100], [120,130], [110,150]]]"/>
+
+    Regions is list of lists [region1, region2, region3, ...] where regionN
+    is disordered list of points: [[1,1], [100,100], [50,50], [20, 70]].
+    
+    If there is only one region in the list, simpler notation can be used:
+    regions="[[10,10], [30,30], [10, 30], [30, 10]]" (without explicitly 
+        setting outer list)
+
+    Returns:
+        True, if click is inside any region or rectangle. Otherwise False.
     """
     snippets = [{'snippet': '''<imageresponse>
-      <imageinput src="image1.jpg" width="200" height="100" rectangle="(10,10)-(20,30)" />
-      <imageinput src="image2.jpg" width="210" height="130" rectangle="(12,12)-(40,60)" />
-      <imageinput src="image2.jpg" width="210" height="130" rectangle="(10,10)-(20,30);(12,12)-(40,60)" />
+      <imageinput src="image1.jpg" width="200" height="100"
+      rectangle="(10,10)-(20,30)" />
+      <imageinput src="image2.jpg" width="210" height="130"
+      rectangle="(12,12)-(40,60)" />
+      <imageinput src="image3.jpg" width="210" height="130"
+      rectangle="(10,10)-(20,30);(12,12)-(40,60)" />
+      <imageinput src="image4.jpg" width="811" height="610"
+      rectangle="(10,10)-(20,30);(12,12)-(40,60)"
+      regions="[[[10,10], [20,30], [40, 10]], [[100,100], [120,130], [110,150]]]"/>
+      <imageinput src="image5.jpg" width="200" height="200"
+      regions="[[[10,10], [20,30], [40, 10]], [[100,100], [120,130], [110,150]]]"/>
     </imageresponse>'''}]
 
     response_tag = 'imageresponse'
@@ -1733,19 +1757,17 @@ class ImageResponse(LoncapaResponse):
 
     def setup_response(self):
         self.ielements = self.inputfields
-        self.answer_ids = [ie.get('id')  for ie in self.ielements]
+        self.answer_ids = [ie.get('id') for ie in self.ielements]
 
     def get_score(self, student_answers):
         correct_map = CorrectMap()
         expectedset = self.get_answers()
-
-        for aid in self.answer_ids:	 # loop through IDs of <imageinput> fields in our stanza
-            given = student_answers[aid]	 # this should be a string of the form '[x,y]'
-
+        for aid in self.answer_ids:	 # loop through IDs of <imageinput>
+        #  fields in our stanza
+            given = student_answers[aid]  # this should be a string of the form '[x,y]'
             correct_map.set(aid, 'incorrect')
-            if not given: # No answer to parse. Mark as incorrect and move on
+            if not given:  # No answer to parse. Mark as incorrect and move on
                 continue
-
             # parse given answer
             m = re.match('\[([0-9]+),([0-9]+)]', given.strip().replace(' ', ''))
             if not m:
@@ -1753,29 +1775,44 @@ class ImageResponse(LoncapaResponse):
                                 'error grading %s (input=%s)' % (aid, given))
             (gx, gy) = [int(x) for x in m.groups()]
 
-            # Check whether given point lies in any of the solution rectangles
-            solution_rectangles = expectedset[aid].split(';')
-            for solution_rectangle in solution_rectangles:
-                # parse expected answer
-                # TODO: Compile regexp on file load
-                m = re.match('[\(\[]([0-9]+),([0-9]+)[\)\]]-[\(\[]([0-9]+),([0-9]+)[\)\]]',
-                             solution_rectangle.strip().replace(' ', ''))
-                if not m:
-                    msg = 'Error in problem specification! cannot parse rectangle in %s' % (
-                        etree.tostring(self.ielements[aid], pretty_print=True))
-                    raise Exception('[capamodule.capa.responsetypes.imageinput] ' + msg)
-                (llx, lly, urx, ury) = [int(x) for x in m.groups()]
-
-                # answer is correct if (x,y) is within the specified rectangle
-                if (llx <= gx <= urx) and (lly <= gy <= ury):
-                    correct_map.set(aid, 'correct')
-                    break
-
+            rectangles, regions = expectedset
+            if rectangles[aid]:  # rectangles part - for backward compatibility
+                # Check whether given point lies in any of the solution rectangles
+                solution_rectangles = rectangles[aid].split(';')
+                for solution_rectangle in solution_rectangles:
+                    # parse expected answer
+                    # TODO: Compile regexp on file load
+                    m = re.match('[\(\[]([0-9]+),([0-9]+)[\)\]]-[\(\[]([0-9]+),([0-9]+)[\)\]]',
+                                 solution_rectangle.strip().replace(' ', ''))
+                    if not m:
+                        msg = 'Error in problem specification! cannot parse rectangle in %s' % (
+                            etree.tostring(self.ielements[aid], pretty_print=True))
+                        raise Exception('[capamodule.capa.responsetypes.imageinput] ' + msg)
+                    (llx, lly, urx, ury) = [int(x) for x in m.groups()]
+
+                    # answer is correct if (x,y) is within the specified rectangle
+                    if (llx <= gx <= urx) and (lly <= gy <= ury):
+                        correct_map.set(aid, 'correct')
+                        break
+            if correct_map[aid]['correctness'] != 'correct' and regions[aid]:
+                parsed_region = json.loads(regions[aid])
+                if parsed_region:
+                    if type(parsed_region[0][0]) != list:
+                        # we have [[1,2],[3,4],[5,6]] - single region
+                        # instead of [[[1,2],[3,4],[5,6], [[1,2],[3,4],[5,6]]]
+                        # or [[[1,2],[3,4],[5,6]]] - multiple regions syntax
+                        parsed_region = [parsed_region]
+                    for region in parsed_region:
+                        polygon = MultiPoint(region).convex_hull
+                        if (polygon.type == 'Polygon' and
+                                polygon.contains(Point(gx, gy))):
+                            correct_map.set(aid, 'correct')
+                            break
         return correct_map
 
     def get_answers(self):
-        return dict([(ie.get('id'), ie.get('rectangle')) for ie in self.ielements])
-
+        return (dict([(ie.get('id'), ie.get('rectangle')) for ie in self.ielements]),
+                dict([(ie.get('id'), ie.get('regions')) for ie in self.ielements]))
 #-----------------------------------------------------------------------------
 # TEMPORARY: List of all response subclasses
 # FIXME: To be replaced by auto-registration

common/lib/capa/capa/templates/crystallography.html

 <section id="inputtype_${id}" class="capa_inputtype" >
-     <div id="holder" style="width:${width};height:${height}"></div>
+    <div class="crystalography_problem" style="width:${width};height:${height}"></div>
+
+    <div class="input_lattice">
+        Lattice: <select></select>
+    </div>
+
     <div class="script_placeholder" data-src="/static/js/raphael.js"></div>
     <div class="script_placeholder" data-src="/static/js/sylvester.js"></div>
-    <div class="script_placeholder" data-src="/static/js/underscore-min.js"></div>
     <div class="script_placeholder" data-src="/static/js/crystallography.js"></div>
 
-
     % if status == 'unsubmitted':
-    <div class="unanswered" id="status_${id}">
+        <div class="unanswered" id="status_${id}">
     % elif status == 'correct':
-    <div class="correct" id="status_${id}">
+        <div class="correct" id="status_${id}">
     % elif status == 'incorrect':
-    <div class="incorrect" id="status_${id}">
+        <div class="incorrect" id="status_${id}">
     % elif status == 'incomplete':
-    <div class="incorrect" id="status_${id}">
-    % endif
-    % if hidden:
-      <div style="display:none;" name="${hidden}" inputid="input_${id}" />
+        <div class="incorrect" id="status_${id}">
     % endif
 
-  <input type="text" name="input_${id}" id="input_${id}" value="${value|h}"
-   % if size:
-   size="${size}"
-   % endif
-   % if hidden:
-    style="display:none;"
-   % endif
-   />
 
-      <p class="status">
+    <input type="text" name="input_${id}" id="input_${id}" value="${value|h}" style="display:none;"/>
+
+    <p class="status">
         % if status == 'unsubmitted':
         unanswered
         % elif status == 'correct':
@@ -38,14 +32,15 @@
         % elif status == 'incomplete':
         incomplete
         % endif
-      </p>
+    </p>
+
+    <p id="answer_${id}" class="answer"></p>
 
-  <p id="answer_${id}" class="answer"></p>
+    % if msg:
+        <span class="message">${msg|n}</span>
+    % endif
 
-  % if msg:
-      <span class="message">${msg|n}</span>
-  % endif
-% if status in ['unsubmitted', 'correct', 'incorrect', 'incomplete']:
-</div>
-% endif
+    % if status in ['unsubmitted', 'correct', 'incorrect', 'incomplete']:
+        </div>
+    % endif
 </section>

common/lib/capa/capa/tests/test_files/imageresponse.xml

@@ -18,4 +18,23 @@ Hello</p></text>
 <text><p>Use conservation of energy.</p></text>
 </hintgroup>
 </imageresponse>
+
+
+<imageresponse max="1" loncapaid="12">
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" rectangle="(490,11)-(556,98)" regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"/>
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" rectangle="(490,11)-(556,98)" regions='[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]'/>
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"/>
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"/>
+<text>Click on either of the two positions as discussed previously.</text>
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" regions="[[[10,10], [20,10], [20, 30]]]"/>
+<text>Click on either of the two positions as discussed previously.</text>
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" regions="[[10,10], [30,30], [15, 15]]"/>
+<imageinput src="/static/Physics801/Figures/Skier-conservation of energy.jpg" width="560" height="388" regions="[[10,10], [30,30], [10, 30], [30, 10]]"/>
+<text>Click on either of the two positions as discussed previously.</text>
+<hintgroup showoncorrect="no">
+<text><p>Use conservation of energy.</p></text>
+</hintgroup>
+</imageresponse>
+
+
 </problem>

common/lib/capa/capa/tests/test_inputtypes.py

@@ -407,13 +407,11 @@ class CrystallographyTest(unittest.TestCase):
     def test_rendering(self):
         height = '12'
         width = '33'
-        size = '10'
 
         xml_str = """<crystallography id="prob_1_2"
         height="{h}"
         width="{w}"
-        size="{s}"
-        />""".format(h=height, w=width, s=size)
+        />""".format(h=height, w=width)
 
         element = etree.fromstring(xml_str)
 
@@ -428,9 +426,7 @@ class CrystallographyTest(unittest.TestCase):
         expected = {'id': 'prob_1_2',
                     'value': value,
                     'status': 'unsubmitted',
-                    'size': size,
                     'msg': '',
-                    'hidden': '',
                     'width': width,
                     'height': height,
                    }

common/lib/capa/capa/tests/test_responsetypes.py

@@ -52,24 +52,57 @@ class ImageResponseTest(unittest.TestCase):
     def test_ir_grade(self):
         imageresponse_file = os.path.dirname(__file__) + "/test_files/imageresponse.xml"
         test_lcp = lcp.LoncapaProblem(open(imageresponse_file).read(), '1', system=test_system)
-        correct_answers = {'1_2_1': '(490,11)-(556,98)',
-                           '1_2_2': '(242,202)-(296,276)',
-                           '1_2_3': '(490,11)-(556,98);(242,202)-(296,276)',
-                           '1_2_4': '(490,11)-(556,98);(242,202)-(296,276)',
-                           '1_2_5': '(490,11)-(556,98);(242,202)-(296,276)',
+        # testing regions only
+        correct_answers = {
+           #regions
+           '1_2_1': '(490,11)-(556,98)',
+           '1_2_2': '(242,202)-(296,276)',
+           '1_2_3': '(490,11)-(556,98);(242,202)-(296,276)',
+           '1_2_4': '(490,11)-(556,98);(242,202)-(296,276)',
+           '1_2_5': '(490,11)-(556,98);(242,202)-(296,276)',
+           #testing regions and rectanges
+           '1_3_1': 'rectangle="(490,11)-(556,98)" \
+           regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"',
+           '1_3_2': 'rectangle="(490,11)-(556,98)" \
+           regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"',
+           '1_3_3': 'regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"',
+           '1_3_4': 'regions="[[[10,10], [20,10], [20, 30]], [[100,100], [120,100], [120,150]]]"',
+           '1_3_5': 'regions="[[[10,10], [20,10], [20, 30]]]"',
+           '1_3_6': 'regions="[[10,10], [30,30], [15, 15]]"',
+           '1_3_7': 'regions="[[10,10], [30,30], [10, 30], [30, 10]]"',
                           }
-        test_answers = {'1_2_1': '[500,20]',
-                        '1_2_2': '[250,300]',
-                        '1_2_3': '[500,20]',
-                        '1_2_4': '[250,250]',
-                        '1_2_5': '[10,10]',
+        test_answers = {
+            '1_2_1': '[500,20]',
+            '1_2_2': '[250,300]',
+            '1_2_3': '[500,20]',
+            '1_2_4': '[250,250]',
+            '1_2_5': '[10,10]',
+
+            '1_3_1': '[500,20]',
+            '1_3_2': '[15,15]',
+            '1_3_3': '[500,20]',
+            '1_3_4': '[115,115]',
+            '1_3_5': '[15,15]',
+            '1_3_6': '[20,20]',
+            '1_3_7': '[20,15]',
                         }
+
+        # regions
         self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_2_1'), 'correct')
         self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_2_2'), 'incorrect')
         self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_2_3'), 'correct')
         self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_2_4'), 'correct')
         self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_2_5'), 'incorrect')
 
+        # regions and rectangles
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_1'), 'correct')
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_2'), 'correct')
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_3'), 'incorrect')
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_4'), 'correct')
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_5'), 'correct')
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_6'), 'incorrect')
+        self.assertEquals(test_lcp.grade_answers(test_answers).get_correctness('1_3_7'), 'correct')
+
 
 class SymbolicResponseTest(unittest.TestCase):
     def test_sr_grade(self):

create-dev-env.sh

@@ -99,7 +99,7 @@ NUMPY_VER="1.6.2"
 SCIPY_VER="0.10.1"
 BREW_FILE="$BASE/mitx/brew-formulas.txt"
 LOG="/var/tmp/install-$(date +%Y%m%d-%H%M%S).log"
-APT_PKGS="pkg-config curl git python-virtualenv build-essential python-dev gfortran liblapack-dev libfreetype6-dev libpng12-dev libxml2-dev libxslt-dev yui-compressor nodejs npm graphviz graphviz-dev mysql-server libmysqlclient-dev"
+APT_PKGS="pkg-config curl git python-virtualenv build-essential python-dev gfortran liblapack-dev libfreetype6-dev libpng12-dev libxml2-dev libxslt-dev yui-compressor nodejs npm graphviz graphviz-dev mysql-server libmysqlclient-dev libgeos-dev"
 
 if [[ $EUID -eq 0 ]]; then
     error "This script should not be run using sudo or as the root user"

docs/source/capa.rst

 *******************************************
 Capa module
 *******************************************
+Contents:
 
 .. module:: capa
 
+.. toctree::
+    :maxdepth: 2
+
+    chem.rst
+
 Calc
 ====
 

docs/source/chem.rst

+*******************************************
+Chem module
+*******************************************
+
+.. module:: chem
+
+Miller
+======
+
+.. automodule:: capa.chem.miller
+    :members:
+    :show-inheritance:
+
+UI part and inputtypes
+----------------------
+Miller module is used in the system in crystallography problems.
+Crystallography is a class in :mod:`capa` inputtypes module.
+It uses *crystallography.html* for rendering and **crystallography.js**
+for UI part.
+
+Documentation from **crystallography.js**::
+
+    For a crystallographic problem of the type
+
+     Given a plane definition via miller indexes, specify it by plotting points on the edges
+     of a 3D cube. Additionally, select the correct Bravais cubic lattice type depending on the
+     physical crystal mentioned in the problem.
+
+    we create a graph which contains a cube, and a 3D Cartesian coordinate system. The interface
+    will allow to plot 3 points anywhere along the edges of the cube, and select which type of
+    Bravais lattice should be displayed along with the basic cube outline.
+
+    When 3 points are successfully plotted, an intersection of the resulting plane (defined by
+    the 3 plotted points), and the cube, will be automatically displayed for clarity.
+
+    After lotting the three points, it is possible to continue plotting additional points. By
+    doing so, the point that was plotted first (from the three that already exist), will be
+    removed, and the new point will be added. The intersection of the resulting new plane and
+    the cube will be redrawn.
+
+    The UI has been designed in such a way, that the user is able to determine which point will
+    be removed next (if adding a new point). This is achieved via filling the to-be-removed point
+    with a different color.
+
+
+
+Chemcalc
+========
+
+.. automodule:: capa.chem.chemcalc
+    :members:
+    :show-inheritance:
+
+Chemtools
+=========
+
+.. automodule:: capa.chem.chemtools
+    :members:
+    :show-inheritance:
+
+
+Tests
+=====
+
+.. automodule:: capa.chem.tests
+    :members:
+    :show-inheritance:
+
+

requirements.txt

@@ -8,11 +8,11 @@ lxml
 boto
 mako
 python-memcached
-python-openid 
+python-openid
 path.py
 django_debug_toolbar
 fs
-beautifulsoup 
+beautifulsoup
 beautifulsoup4
 feedparser
 requests
@@ -37,7 +37,7 @@ django-jasmine
 django-keyedcache
 django-mako
 django-masquerade
-django-openid-auth 
+django-openid-auth
 django-robots
 django-ses
 django-storages
@@ -54,3 +54,4 @@ dogstatsd-python
 # Taking out MySQL-python for now because it requires mysql to be installed, so breaks updates on content folks' envs.
 # MySQL-python
 sphinx
+Shapely